Haemogregarina bigemina is one of the most prevalent haemogregarines of marine fishes and has long been considered an enigmatic and cosmopolitan species. However, to determine whether H. bigemina truly represents a single global species, or whether it should be partitioned into several species or subspecies, and to confirm its taxonomic status among the Haemogregarina, molecular analysis is required. Here, we provide the first molecular characterisation of H. bigemina from one of its type hosts, Lipophrys pholis, in the UK using 18S rDNA sequences. Phylogenetic and p-distance comparisons of the newly generated H. bigemina sequences with those published from other haemogregarine taxa and related apicomplexans suggest that H. bigemina falls outside of the “Haemogregarina” clade as well as the Adeleorina altogether, forming a separate apicomplexan marine clade, and appears to be in fact more closely related to other non-haemogregarine Apicomplexa genera. Further work including sequences of H. bigemina and H. bigemina-like parasites observed from fishes in other localities is now needed to investigate this further.