Previous surveys have shown that most populations of Daphnia pulex in the Great Lakes watershed reproduce by obligate parthenogenesis. Cyclically parthenogenetic populations, in which there is sexual reproduction, are confined to only a few isolated areas. The present study assessed genetic variation within and among 11 cyclically parthenogenetic populations. The results for six polymorphic enzyme loci showed that variation within the populations conformed to that expected for populations with frequent sexual reproduction. Seven of the populations sampled in 1988 were previously sampled in either 1985 or 1986. Allele frequencies determined in 1988 were very similar for the same loci sampled in previous years, and there was no evidence for the invasion of these populations by obligate parthenogens during this period. There was no significant difference in the average heterozygosity among the 11 populations. Although significant heterogeneity in allele frequencies was detected among the 11 populations for all six loci (average FST = 0.18), the pattern of population differentiation was only very weakly related to geographic distance. An analysis of gene diversity showed that the level of population differentiation for cyclically parthenogenetic D. pulex is much lower than has been observed for most other cladoceran species.