Bovine babesiosis is a serious threat to the cattle industry. We prepared blood DNA samples from 13 cattle with clinical babesiosis from the Badulla ( = 8), Jaffna ( = 3), and Kilinochchi ( = 2) districts in Sri Lanka. These DNA samples tested positive in PCR assays specific for ( = 9), ( = 9), and ( = 1). Twelve cattle were positive for and/or One cow was negative for the tested species but was positive for on microscopic examination; the phylogenetic positions of 18S rRNA and cytochrome oxidase subunit III gene sequences suggested that the cow was infected with sp. Mymensingh, which was recently reported from a healthy cow in Bangladesh. We then developed a novel sp. Mymensingh-specific PCR assay and obtained positive results for one other sample. Analysis of gene sequences from the cow with positive -specific PCR results demonstrated that the animal was infected not with but with sp. Hue-1, which was recently reported from asymptomatic cattle in Vietnam. The virulence of sp. Hue-1 is unclear, as the cow was coinfected with and However, sp. Mymensingh probably causes severe clinical babesiosis, as it was the sole species detected in a clinical case. The present study revealed the presence of two bovine species not previously reported in Sri Lanka, plus the first case of severe bovine babesiosis caused by a species other than ,, and .