The interpretation of low F-ST values as evidence of high levels of gene fl
ow among habitat fragments may be confounded by population genetic structur
es that are indicative of historical rather than present-day levels of gene
flow. We examined the genetic structure of 23 populations of Baetis alpinu
s (Insecta: Ephemeroptera) living in alpine streams fragmented by lakes (ap
proximate to 10 000 years old), reservoirs (approximate to 100 years old),
and in nonfragmented streams, to examine if lakes act as barriers to gene f
low and to investigate the temporal resolution of allozyme markers. Estimat
es of gene flow indicated little or no genetic divergence along four nonfra
gmented reference streams and across two lakes and two reservoirs (F-ST = 0
.004-0.041), but marked differentiation across four lakes (F-ST = 0.092-0.3
62) and across one reservoir that was a lake enlarged by a dam (F-ST = 0.07
5). Differentiation was unrelated to distance between fragments, but occurr
ed only in lakes found in valleys that have been ice-free throughout the Ho
locene. We suggest that standing water bodies act as barriers to gene flow
in B. alpinus and that low F-ST values observed between fragments separated
by reservoirs do not indicate high levels of gene flow but rather show tha
t genetic differentiation was not detectable within the first 100-1000 year
s of habitat fragmentation.