The sequences of 10 conservative regions (CR) of minicircles of 6 selected isolates of freshwater fish trypanosomes have typical organization of this region with high degree of sequence conservation. The comparison with CRs of other trypanosomatids showed that freshwater fish trypanosomes represent a compact separate group within the genus Trypanosoma. The alignment of all sequences obtained revealed, however, the existence of 2 types of CRs in sequenced minicircles, with the differences concentrated in a short region. Taxonomic consequences of these results are discussed.