Babesia species (Piroplasmida) are hemoparasites that infect erythrocytes of mammals and birds and are mainly transmitted by hard ticks (Acari: Ixodidae). These hemoparasites are known to be the second most common parasites infecting mammals, after trypanosomes, and some species may cause malaria-like disease in humans. Diagnosis and understanding of Babesia diversity increasingly rely on genetic data obtained through molecular techniques. Among hard ticks, several Ixodes species are known vectors of Babesia microti-like species in the Northern Hemisphere. Recently, Ixodes and Amblyomma ticks have been recorded parasitizing the Andean bear (Tremarctos ornatus) in Ecuador. Previous reports have suggested babesiosis in a fatal case of this threatened bear species in that country. This study aimed to detect Piroplasmida DNA in hard ticks collected from Andean bears at two sites in Ecuador. This species plays a critical role as an ecological engineer and a seed disperses, contributing significantly to the maintenance and health of Andean ecosystems. Twelve ticks screened with conventional PCR and Piroplasmida DNA was amplified from one Ixodes montoyanus tick collected from a free-living female Andean bear at Llanganates National Park. Two Babesia sequences were characterized: one for the 18 S ribosomal rRNA gene and another for the cytochrome c oxidase 1 gene. Phylogenetic analyses for both loci placed these sequences within the B. microti-like clade. This study reports a novel B. microti-like genotype identified in an I. montoyanus parasitizing a female Andean bear, contributing to the knowledge of the diversity of this group in South America. Given their conservation status, future epidemiological surveillance of Babesia and other tick-borne infectious agents in Andean bears is needed.