RAPD-PCR polymorphisms were used to examine breeding structure in three species of snow pool Aedes mosquitoes across three river drainages in northern Colorado. Larvae were collected from four snow pools for Aedes cataphylla Dyar, seven pools for A. hexodontus Dyar and six pools for A. pullatus (Coquillet). Polymorphisms were scored at 47–48 RAPD loci in each species. To test for isolation by distance, FST/(1−FST) values between pairs of pools were plotted against geographical distances and subjected to a Mantel test with 1000 random permutations. FST values were independent of geographical distances in A. cataphylla and A. hexodontus but were somewhat correlated in A. pullatus suggesting isolation by distance in this species. A cluster analysis was performed on pair-wise FST values among pools including seven pools that were sampled in both 1994 and 1995. Bootstrap analysis indicated that pools clustered across drainages and generally independently of geographical proximity. However, there was consistent support for clustering of larvae collected from the same pool across years in A. cataphylla and in high altitude collections of A. pullatus. Mountains do not appear to act as major barriers to gene flow in any of these species. Instead, seasonal differences in adult emergence may serve as barriers to migration among A. pullatus and A. cataphylla populations. Larvae of A. hexodontus are distributed continuously in grassy pools along the banks of rivers and genetic drift probably occurs through random larval mortality when these pools are washed out during spring run-off.