I'm going to list every endemic life marked with a special border in the Hunter's Notes.

Terrestrial Life

• Pilot Hare: a red-pink hare found during clear weather in the Ancient Forest (area 1, area 2, area 8, and area 15) and the Wildspire Waste (area 1, area 2, and area 4).
• Moonlight Gekko: a glowing purple reptile, found next to Brightmoss in the Rotten Vale (area 11 and area 13) and the Elder's Recess (area 8 and area 8 again, inside the camp).
• Wiggler Queen: an orange variant of the regular Wiggler, found during the night in the Coral Highlands (area 1 and area 3).
• Emerald Helmcrab: a large, green helmcrab, found in the Wildspire Waste (area 4 and area 10) and the Rotten Vale (area 6 and area 9), more commonly during bad weather.
• Shiny Gold Helmcrab: a very large and shiny helmcrab, found on the sunny ledges in area 1 (screenshot 1*, screenshot 2) and area 2 (screenshot) of the Caverns of El Dorado.
  _{* You can check for this guy in the opening cutscene: screenshot}
• Gold Calappa: a large golden crab with a red gem on its carapace, found near Kulve's tunnels in area 1 of the Caverns of El Dorado (screenshot 1, screenshot 2, screenshot 3, screenshot 4).
• Tsuchinoko: a flat, crawling snake found near the cannons (screenshot 1, screenshot 2, screenshot 3, screenshot 4), in the upper parts of area 1 (screenshot 1, screenshot 2*, screenshot 3), down the long slide from area 1 to area 2 (screenshot), and at the passage from area 2 to area 3 (screenshot) in the Caverns of El Dorado. Also found in the camp area of the Origin Isle.
  _{* Walk to the left side of the ledge to get it to notice you}

Aquatic Life

• Petricanth: a dark fish with glowing blue spots, found in the Rotten Vale (area 15, near the Plunderers) and the Elder's Recess (inside the camp in area 8). Unlocks the "A Living Fossil" achievement.
• King Marlin: a large swordfish, found in the ocean of area 4 of the Ancient Forest and in area 9 of the Hoarfrost Reach.

Airborne Life

• Phantom Flutterfly: a single, large, green and yellow butterfly found in area 6 and area 11 of the Ancient Forest.
• Augurfly: a blue-winged insect, found in the Ancient Forest (area 11, area 14, and area 16), the Wildspire Waste (area 2, area 10, and area 11), the Coral Highlands (area 3, area 5, area 7, area 8, and area 14), the Rotten Vale (area 11, area 12, and area 15), and the Elder's Recess (area 7, area 8, and area 16). More common while it's raining.
• Dapper Coralbird: a darker, almost purple Coralbird found together with Elegant Coralbirds in area 1, area 1 again, area 5, area 5 again, and area 6 of the Coral Highlands.

Treetop Life

• Forest Pteryx: a bright, blue and red flying beast found leaping from tree to tree in area 5 and area 15 of the Ancient Forest.
• Gold Hercudrome: a gold beetle, found during the night on trees in the Ancient Forest (area 6) and the Wildspire Waste (area 5).
• Prism Hercudrome: an iridescent beetle, found at dusk and dawn in the Ancient Forest (area 1), the Wildspire Waste (area 10), the Coral Highlands (area 11), the Rotten Vale (area 11), and the Elder's Recess (area 3). Unlocks the "Rainbow Bright" achievement.

Unclassified Life

• Downy Crake: a small, white, round bird, found in flocks on the back of Aptonoth in the Ancient Forest (screenshot 1, screenshot 2), on the back of Apceros in the Wildspire Waste (screenshot 1, screenshot 2, screenshot 3), and on the back of Grandfather Mantagrell in the Coral Highlands (screenshot 1, screenshot 2, screenshot 3). Ghillie Mantle is highly recommended. Unlocks the "Suggles for All" achievement.
• Bristly Crake: a large, black bird, found on the back of Mosswine in the Rotten Vale (screenshot 1, screenshot 2), and on the back of Gastodon in the Elder's Recess (screenshot 1, screenshot 2, screenshot 3). Ghillie Mantle is highly recommended. Also found on the back of Soldier Helmcrabs in area 12 of the Guiding Lands. It appears it might only spawn when the Rotten area is at least level 5. Unlocks the "Bristles for All" achievement.
• Cactuar: a cactus with legs, found as a hazard in area 4, area 7, and area 8 of the Wildspire Waste. Shows up on the map.
• Cactuar Cutting: a cactus with legs, found running around area 1, area 4, area 4 again, on top of area 5, area 6, area 6 again, and area 8 of the Wildspire Waste.
• Flowering Cactuar Cutting: a cactus with legs and a pink flower on its head, found hopping on top of area 5 or running around the cacti in area 6 of the Wildspire Waste.
• Nekker: a short bipedal creature that spawns during the night in area 2 of the Ancient Forest, when Great Jagras regurgitates food to give to its young (screenshot).

In addition, some fish can spawn in a Great Size variant, which offers more research points and better items:

Great Fish

• Great Pink Parexus: found in the Ancient Forest (area 1, area 4, area 9, area 11, area 11 again, area 11 AGAIN, and area 14), the Wildspire Waste (area 6), the Coral Highlands (area 6, area 7, and area 11), the Rotten Vale (area 9 and area 10), and the Elder's Recess (area 1, area 1 again, area 7, and area 8).
• Great Burst Arowana: found in the Ancient Forest (area 1, area 11, area 11 again, and area 14), the Wildspire Waste (area 1, area 10, and area 10 again), the Coral Highlands (area 6 and area 11), the Rotten Vale (area 9 and area 10), the Elder's Recess (area 8), and the Hoarfrost Reach (area 8).
• Great Bomb Arowana: found in the Ancient Forest (area 11, area 11 again, and area 14), the Wildspire Waste (area 10 and area 10 again), the Coral Highlands (area 6), the Rotten Vale (area 9 and area 10), and the Elder's Recess (area 8).
• Great Whetfish: found in the Ancient Forest (area 1, area 4, area 9, area 11, and area 11 again), the Wildspire Waste (area 1 and area 6), the Coral Highlands (area 7 and area 11), the Rotten Vale (area 9 and area 10), the Elder's Recess (area 1, area 1 again, and area 8), and the Hoarfrost Reach (area 8 and area 12).
• Great Gastronome Tuna: found in the Ancient Forest (area 4), the Wildspire Waste (area 6), the Rotten Vale (area 10), the Elder's Recess (area 8), and the Hoarfrost Reach (area 9).
• Great King Marlin: found in the Ancient Forest (area 4) and the Hoarfrost Reach (area 9).
• Great Goldenfish: found in the Coral Highlands (area 14), the Rotten Vale (area 10, area 15 and area 15 again), the Elder's Recess (area 8), and the Hoarfrost Reach (area 8 and area 8 again).
• Great Platinumfish: found in the Elder's Recess (area 7 and area 8) and the Hoarfrost Reach (area 8).
• Great Goldenfry: found in the Ancient Forest (area 11, area 11 again), the Wildspire Waste (area 6), the Coral Highlands (area 14), and the Rotten Vale (area 15).
• Great Sushifish: found in the Ancient Forest (area 1, area 4, area 9, area 11, area 11 again, area 11 AGAIN, and area 14), the Wildspire Waste (area 1, area 6, and area 10), the Coral Highlands (area 6, area 7, and area 11), the Rotten Vale (area 9 and area 10), the Elder's Recess (area 1, area 1 again, area 7, and area 8), and the Hoarfrost Reach (area 9, area 12, and area 15). Uniquely, there are two different spawns in the same spot in area 9!
• Great Gunpowderfish: found in the Coral Highlands (area 6 and area 7), the Rotten Vale (area 9), and the Elder's Recess (area 8).

In addition to being larger, Great Size fish are also noticeably brighter than their regular counterparts.

When a Great Size fish spawns, it appears in addition to all the fish that are normally found at a fishing spot. If you see more than the usual number of fish, one of them is a Great fish.

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Iceborne exclusive content

Eat for Felyne Zoomaster!! Combine it with the daily skill Felyne Biologist for even better chances.

Terrestrial Life

• Goldspring Macaque: a short, golden monkey with a three-ended tail that likes relaxing in hot springs. Found in clear weather in area 2 of the Hoarfrost Reach. Can also be found in area 6, but I have only confirmed this spawn in the Monkey Business event quest. Unlocks the "Golden Gleam" achievement.
• Arrowhead Gekko: a round, blue lizard with a head shaped like a triangle. Spawns on days of abundant resources like fruit or mushrooms, and will guide the player to the one special spawn that appears on those days. Found in the Ancient Forest (leads the player from area 17 to the unique Flower Bed, and from area 11 to the unique... Unique Mushroom Colony), the Wildspire Waste (leads the player from area 5 to the unique Round Cactus, and from area 15 to the unique Tough-skinned Fruit), the Coral Highlands (leads the player from area 13f to the unique Pearl Oyster, and from area 9 to the unique Conch Shell), the Rotten Vale (leads the player from area 1 to the unique Ancient Fossil, and from area 10 to the unique Crimson Fruit), and the Elder's Recess (leads the player from area 8 to the unique Beryl Deposit, and from area 16 to the unique Amber Deposit). Unlocks the "Friendly Pointer" achievement.

Aquatic Life

• Sealord's Crestfish: a very long fish with glowing appendages, found during the night in area 8 of the Hoarfrost Reach. Unlocks the "Submerged Mystery" achievement.

Treetop Life

• Blue Diva: a blue bird with a long tail, constantly singing. Found in the Ancient Forest (area 11, area 17, and area 17 again), the Wildspire Waste (three¹ different spots¹ in area 5), and the Coral Highlands (a total of four different spots in area 6). Can't be caught in some of these locations, as they are too far to reach with the Capture Net. However, instead of disappearing when startled, the Blue Diva will simply move to a different location in the same map. Keep chasing it! Unlocks the "Sweet Melody" achievement.

Unclassified Life

• Wintermoon Nettle: a huge jellyfish-like creature, floating around the very top of area 13 of the Hoarfrost Reach very rarely during clear nights. Unlocks the "Celestial Illusion" achievement.
• Moly: a mole-like creature, found digging out of the ground in area 6, area 7, area 8, area 9, area 10, area 11, area 12, area 13, area 14, area 15, area 16, and another spot in area 16 of the Guiding Lands. Unlocks the "Deft Digger" achievement.
• Mossy Moly: a Moly covered in flowering moss, found with regular Moly in area 6 and area 7 of the Guiding Lands at level 5 of the Forest Region.
• Rocky Moly: a Moly wearing a hard hat, found with regular moly in area 8 and area 9 of the Guiding Lands at level 5 of the Wildspire Region.
• Fluffy Moly: a Moly covered in pink, fluffy fur, found with regular Moly in area 10 and area 11 of the Guiding Lands at level 5 of the Coral Region.
• Spiny Moly: a Moly covered in black fur and with shawp claws, found with regular Moly in area 12 and area 13 of the Guiding Lands at level 5 of the Rotted Region.
• Rowdy Moly: a Moly with fiery red fur, found with regular Moly in area 14 and area 15 of the Guiding Lands at level 5 of the Volcanic Region.
• Frosty Moly: a white Moly, shivering and sniffling, found with regular Moly in area 16 and another spot in area 16 of the Guiding Lands at level 5 of the Tundra Region.

Catching any rare Moly unlocks the "Creatures of the Earth" achievement.

Great Fish

• Great Glass Parexus: found in the Hoarfrost Reach (area 8, area 8 again, area 12, and area 15).

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1: spots originally discovered by Steam user Destrukshor