Estimates and variances of diversity and differentiation measures in s
ubdivided populations are proposed that can be applied to haplotypes p
es (ordered alleles such as DNA sequences, which may contain a record
of their own histories). Hence, two measures of differentiation can be
compared for a single data set: one (G(ST)) that makes use only of th
e allelic frequencies and the other (N-ST) for which similarities betw
een the haplotypes are taken into account in addition. Tests are propo
sed to compare N-ST and G(ST) with zero and with each other. The diffe
rence between N-ST and G(ST) can be caused by several factors, includi
ng sampling artefacts, unequal effect of mutation rates and phylogeogr
aphic structure. The method presented is applied to a published data s
et where a nuclear DNA sequence had been determined from individuals o
f a grasshopper distributed in 24 regions of Europe. Additional insigh
ts into the genetic subdivision of these populations are obtained by p
rogressively combining related haplotypes and reanalyzing the data eac
h time.