from the comprehensibility of the sentence, it makes no difference.
But, since you have started with 'their long black hair' it makes more sense to end with 'their heads'
If you want to avoid this sort of pitfall, you'll have to re-phrase.
Something on the lines of:
"A distinctive feature of the bonobo is the long black hair on the head (or perhaps: head-hair), parted in the middle".