Swamp buffalo (Bubalus bubalis) is important livestock by farmers at Kalimantan Island for meat production and drought purposes. This research was carried out to classify buffalo (about 3.5 years of age) based on their morphometrical measurements. The animals in this study were collected from North Kalimantan (NK), East Kalimantan (EK), and South Kalimantan (SK) regions. A Total of 50 animals (25 males and 25 females) were collected from each region. Thus, eight morphometrics of withers height (WH), body length (BL), chest girth (CG), shoulder width (SW), chest depth (CD), rump height (RH), rump width (RW), and rump length (RL) were measured in this study. Research findings showed that four morphometrics of WH, RL, CG, and BL were described as the discriminating variables. According to the Euclidean distance, the buffalo from EK and SK were grouped into a similar cluster. Meanwhile, the buffalo from NK was grouped into a different cluster. Therefore, the observed morphometrics in this study was capable to classify buffalo at NK (100%), EK (66%), and SK (70%) into their original population group. In conclusion, the buffalo at EK and SK regions have an imminent genetic relationship. Moreover, a study to classify buffalo using cranial measurements is important to support this finding due to mtDNA analysis.