Carriers of bovine anaplasmosis in Northern Kerala, South India were detected using conventional microscopical and molecular techniques. PCR-RFLP and nested PCR techniques were used for detection of Anaplasma marginale and Anaplasma bovis respectively and the PCR products were confirmed by sequencing. Out of 150 samples tested, 25 were detected positive for A. marginale and five for A. bovis based on molecular tests. The inclusion bodies of A. marginale could be detected by microscopy in two blood smears after staining by giemsa while acridine orange staining detected three smears positive. The data clearly suggest the higher sensitivity of molecular techniques for diagnosis of these diseases.