The Heteroceridae is a taxonomically difficult family of small (2-7 mm) beetles that live in self-constructed feeding tunnels along the shores of fresh and brackish waters worldwide. Traditional classifications of Heteroceridae typically accept only five genera (Heterocerus, Micilus, Augyles, Phyrites and Elythomerus), but the most recent revision of the family recognized nineteen (Pacheco, 1964), with twelve segregated from the type genus alone. These new genera, which are based on characters of the male genitalia, have not been widely accepted. In order to gain a better understanding of generic limits and relationships, a phylogenetic study using nuclear 28S rDNA and EF-1α gene sequences was undertaken. Phylogenetic analyses support (100% bootstrap) the Heteroceridae as monophyletic, and indicate (83% bootstrap) that it is sister to the Limnichidae within the superfamily Byrrhoidea, a relationship not resolved by a previous morphological study (Lawrence et al., 1995). Within Heteroceridae, analyses firmly position (100-99% bootstrap) Tropicus pusillus and Centuriatus auromicans successively as sisters to a strongly supported (94% bootstrap) terminal clade containing all of the genera segregated from Heterocerus s.l. by Pacheco. Relationships within this clade indicate that the genera Neoheterocerus and Lanternarius sensu Pacheco are unnatural as circumscribed, suggesting that the traditional classification of the family may better reflect relationships. Attempts to increase taxonomic sampling and to add further markers are currently under way.