Microsatellite loci consisting of (CA)n repetitive arrays were obtained from three species of marine turtle, and primers were designed to test for polymorphism within species and the persistence of microsatellites across species. Homologous loci were found in each test of six marine species within two families (Cheloniidae and Dermochelyidae), as well as in a freshwater species (Emydidae, Trachemys scripta), which indicates a conservation of flanking sequences spanning approximately 300 million years of divergent evolution. The persistence of homologous microsatellites across marine turtles was confirmed by direct sequencing of loci across species and by the discovery of polymorphism in 24 of 30 cross species tests. The conservation of flanking sequences could be due to a slow rate of base substitution in turtle nuclear DNA, as previously reported for mtDNA. In contrast, the presence of up to 25 alleles per locus per species indicates that the replication slippage events responsible for changes in allele length operate as in mammals. Comparisons of alleles among species revealed that alleles of the same length may not be homologous due to mutations within the flanking sequences. Levels of heterozygosity were consistently higher in species from which the primers were designed, which suggests problems with cross-species comparisons of variability. Within species, microsatellite variation between divergent populations was consistent with results from previous mtDNA studies indicating the usefulness of microsatellites for comparing male- versus female-mediated gene flow.