In spite of their abundance, widespread distribution and medical importance, the phylogenetic relationships among Biomphalaria snails have received relatively little attention. We have collected and studied 29 populations of snails obtained from different localities from Brazil. We have sequenced the ribosomal DNA second internal transcribed spacer (ITS2) from the following Biomphalaria species: B. glabrata, B. tenagophila tenagophila, B. occidentalis, B. straminea, B. peregrina, B. kuhniana, B. schrammi, B. amazonica, B. oligoza, B. intermedia and an outgroup species Helisoma duryi. The sequence from each species is unique. Three different methods of phylogenetic reconstruction were used (distance, maximum parsimony and maximum likelihood). The resulting phylogenetic trees obtained by these methods basically support current systematic relationships based on morphological characters alone. This study demonstrates that the ITS2 region contains markers useful for identification and determination of relationships among Biomphalaria species.