What is neutral genetic differentiation?

Neutral genetic variation is variation that has no effect on fitness. I suggest reading more about neutral theory on wikipedia.

Neutral genetic differentiation is a way of talking about neutral genetic variation that follows some historical pattern, for example two populations isolated from each other for a long time will show neutral genetic differentiation even if they are individually in Hardy-Weinberg equilibrium. In other words, the two populations will have somewhat different allele frequencies from each other for no reason related to natural selection but rather because of random sampling and genetic drift over time.

It is generally thought that most genetic variation is neutral or nearly neutral. For example, most of the human genome is useless DNA or genomic parasites such as transposons. Almost all of the genetic variation that happens in those regions is not important to human fitness, in other words it is "neutral".