Bodonids, together with parasitic trypanosomatids, constitute a unique flagellate group with unclear relationships among taxa. To get a better understanding of bodonid relationships, a new strain of Bodo designis (Bodo designis DH) was isolated and its small subunit rRNA gene was sequenced. Phylogenetic analyses were performed using parsimony and evolutionary distance methods based on both complete sequences and conserved positions. Tree topologies showed a basal dichotomy in all obtained trees. However, apparent discrepancies were found between trees derived using different criteria. The relationships between trypanosomatids and bodonids remain unsolved. Within the bodonid subtree, the polyphyly of genus Bodo was confirmed and the separation of haematozoic Cryptobia spp. from the non-haematozoic Cryptobia helicis as different genera is considered premature. In addition, it seems that using SSU rRNA gene sequences as a phylogenetic marker is not fully satisfactory in this group.