Introduction Babesiosis is a tick-borne hemo-parasitic disease of domestic and wild animals. Parasites causing babesiosis are considered to infect only specific hosts but some sporadic reports in recent past are in strong disagreement with their host specificity. This is the first report of a domestic cat being naturally infected with a novel Babesia sp. in India. Methods Blood samples collected from dogs (n = 6) and a 3-month-old cat, with clinical symptoms of babesiosis, were submitted to two different laboratories for hematology analysis, light microscopical examination, and molecular confirmation of Babesia sp. using PCR, sequencing, and phylogenetic analysis. Results Hematological alterations noticed in canine and feline samples were severe anemia and thrombocytopenia. Pearshaped merozoites were visualized on light microscopic examination of both canine and feline blood smears. Size of the merozoites in feline blood sample was smaller when compared to canine samples. Molecular analysis using Babesia speciesspecific primers showed that all canine samples were positive for B. vogeli and feline sample was negative for B. canis, B. rossi, and B. vogeli infecting dogs. Amplification and sequencing of full-length ssrRNA using universal apicomplexan primers followed by molecular and phylogenetic analysis revealed that the Indian domestic cat was infected with a novel Babesia sp. Conclusion This work presents the first molecular and phylogenetic evidence of a novel Babesia sp. causing feline babesiosis in a naturally infected domestic cat in India. We propose to name this novel species as Babesia panickeri sp. nov.