Current myxozoan phylogeny relies mostly on single 18S rDNA or concatenated analysis of a limited number of 18S + 28S rDNA and exceptionally EF-2 gene sequences. Although these widely-used markers support particular phylogenetic relationships, they are not sufficient to reconstruct the pattern of some early branching nodes, important for the understanding of the main phylogenetic trends of Myxozoa. The present study describes new potential phylogenetic markers nematogalectin genes, which are unique cnidarian-specific genes. Phylogenetic reconstruction based on nematogalectins showed congruency with 18S rDNA based phylogenies and concatenated analysis of 18S rDNA and nematogalectins revealed better support of early branching nodes in the myxozoan tree. Recently published and newly obtained data of these cnidarian-specific genes represent important insights into the phylogeny of Myxozoa