The systematic relationships among 12 species of the intertidal pulmonate limpet, Siphonaria were assessed using the technique of Random Amplified DNA fingerprinting. Previous systematic relationships proposed on the basis of morphology were confirmed for nine of the species considered. A strong systematic basis to mode of larval development (planktonic or direct development) was revealed. The subgenus Patellopsis includes both direct-developing and planktonic-developing species but these nested separately in the classification analysis, suggesting that the subgenus may be polyphyletic. The status of two species in the subgenus Sacculosiphonaria was unclear, but one, the direct-developer Siphonaria compressa, nested with the direct-developing species of the Patellopsis clade. Re-assigning S. compressa to the subgenus Patellopsis would resolve the anomaly of having both developmental modes within Sacculosiphonaria and would be consistent with the DNA findings. In contrast to analyses based on total cellular proteins, DNA analysis indicates that within-population variation was greatest among direct-developing species. This was unexpected and difficult to explain as one anticipates easier distribution of planktotrophic than direct-developing larvae and, thus, greater genetic diversity within populations of planktonic-developing species. One possible explanation is that low levels of gene flow between direct-developers cause small-scale founder effects in sub-populations, thus increasing the overall genetic diversity of the whole population. Within-population variation was highest for the direct-developer, S. compressa, which is not only the smallest and presumably is the least dispersive species examined, but is the species with the most restricted distribution. It is believed to be endemic to a single location in South Africa.