Parasites from diverse hosts morphologically identified as Babesia microti have previously been shown to belong to a paraphyletic species complex. With a growing number of reports of B. microti-like parasites from across the world, this paper seeks to report on the current knowledge of the diversity of this species complex. Phylogenetic analysis of 18S rDNA sequences obtained from GenBank shows that the diversity of the B. microti species complex has markedly increased and now encompasses at least five distinct clades. This cryptic diversity calls into question much of our current knowledge of the life cycle of these parasites, as many biological studies were conducted before DNA sequencing technology was available. In many cases, it is uncertain which B. microti-like parasite was studied because parasites from different clades may occur sympatrically and even share the same host. Progress can only be made if future studies are conducted with careful attention to parasite identification and PCR primer specificity.