A study was carried out to assess the variation in morphological characteristics of four strains (namely, Pare, Gogo, Sukuma and Sonjo) of Small East African (SEA) goat breed in four regions of Tanzania as a first step towards their characterization. A total of 349 mature animals (85 to 92 animals per strain) were randomly sampled from 120 households located in the four regions. For each external qualitative traits (coat color and pattern, hair type and size, presence of wattles and beards, horn size, shape and orientation, ear size and orientation and facial and back profiles) and quantitative traits (body weight, heart girth, height at wither, body length, chest depth, rump height, ear length and horn length) were recorded. Discriminant, cluster and principal component analyses were used to classify the four SEA strains based on morphometric traits. Results for body measurements show that Pare goats had the largest body weight (29.8 ± 0.50 kg), heart girth (72.3 ± 0.51 cm), height at wither (61.4 ± 0.43 cm), body length (53.9 ± 0.51) and rump height (63.4 ± 0.60 cm) , followed by Gogo goats whereas Sukuma and Sonjo goats were the smallest and lightest. Sexual dimorphism was evident for all the body measurements with males being bigger and heavier than females in all populations. Correlations among morphometric variables were significant for most of the pairs of variables tested, the strongest being between body weight and heart girth (r = 0.70), rump height and wither height (r = 0.60) and body weight and chest depth (r = 0.51). Pare (39.6%) and Gogo (40.2%) were predominantly white coloured while Sonjo were red coloured (85.4%) and Sukuma had black and white colour (66.7%). Almost all goats were horned and did not have wattles and the majority of them had medium sized and horizontally oriented ears. Chest depth and body weight were the most powerful discriminating traits in separating the four goat strains. The squared mahalanobis distance based on morphological traits was largest between Pare and Sukuma goats (5.45) and smallest between Pare and Gogo goats (0.94). Cluster analysis revealed two separate groups; a group for Pare goats and another group comprised Gogo, Sonjo and Sukuma goats. A test for assignment of individual animals to their respective strain showed that most Sonjo (75.3%), Sukuma (70.5%) and Pare (67.9%) goats were assigned to their source populations while most of the Gogo goats (51.1%) were mis-assigned to other populations. It is concluded that the four strains of SEA goat breed are heterogeneous populations with large variability in morphological features and they could best be differentiated by chest depth, body weight and coat colour.