Morphological conservatism combined with intraspecific variability has obstructed studies of speciation and species boundaries among marine meiofauna. Ototyphlonemertes is a genus of meiofaunal nemerteans inhabiting the interstitial spaces of marine sediments. Its members lack pelagic larvae and dispersal potential is believed to be poor. A phylogeographic study of Ototyphlonemertes fila is presented using mitochondrial (cox3) and nuclear (ISSR) molecular markers. Deep genetic divergence (approximately 18% in cox3) was observed between sympatric mitochondrial lineages in Florida. This divergence was reflected in the nuclear marker as well, suggesting the presence of two cryptic species. The first contains Florida and New England populations separated by 3% cox3 sequence divergence and showing no evidence of ongoing gene flow. The second contains two codistributed mitochondria1 clades in Florida separated by 3% cox3 sequence divergence and showing exchange of nuclear alleles. Surprisingly, relatively little fine-scale structuring was found, suggesting that passive dispersal is significant over moderate geographical distances.