The research aim was to study the variance of some morphometric characteristics and morphology of Moa buffalo, and the genetic relationships analysis between buffalo subpopulations in Moa Island. Characterization was by using 174 buffalos from any group of ages and sex that were collected from West area (Werwaru, Patti), Central area (Syota, Klis) and East area (Tounwawan, Poliwu). The variables observed were morphometric characters (body weight, shoulder height, body length, chest width, chest depth, chest girth, skull length, skull width, skull height, ear width, ear length, cannon girth, horn length, horn girth and distance between horns), body morphology characters (horn position, head color, body color and scheme of body color), and genetic distance between buffalo subpopulations. Body morphometric data were analyzed using mean, standard deviation and variance coefficient. Body morphology data were analyzed using relative frequencies. The genetic distance was analyzed using canonical discriminant function through Mahalanobis distance approach and by making phylogeny using UPGMA method. The result indicated that variation of body morphometric was related to production performance, variation of color and color scheme of body. Based on genetic distance, central and west subpopulations were the nearest where West subpopulation was isolated from Central and East subpopulation.