PURPOSE: To investigate the seroprevalence and molecular characterization of Anaplasma parasites in mithun (Bos frontalis) and their tick vectors in Nagaland and Arunachal Pradesh, India using serological and molecular methods. METHODS: Mithun sera were screened for Anaplasma antibodies using a competitive ELISA targeting the MSP5 antigen. Blood samples and ticks collected from mithun were analyzed using PCR targeting the RNA polymerase subunit beta (rpoB) gene for Anaplasma species detection, followed by sequencing and phylogenetic analysis of positive samples. RESULTS: Serological testing detected Anaplasma antibodies in 11.90% (5/42) of tested mithun. PCR analysis of 358 mithun blood samples identified eight animals (2.23%) positive for A. marginale, with identity confirmed through sequencing and phylogenetic analysis. Among the collected ticks, Anaplasma was detected in one R. microplus specimen (1/340), while all Amblyomma spp. (n = 25) tested negative. Phylogenetic analysis of the rpoB gene sequences showed the mithun isolates clustering with A. marginale reference sequences from diverse regions. CONCLUSION: This study provides the first documented evidence of A. marginale infection in mithun populations and associated ticks in Northeast India, supported by molecular, serological and phylogenetic analyses. The findings underscore the importance of multi-faceted diagnostic approaches, targeted vector control, and ongoing surveillance to address regional disease risks.