The majority of Tswana sheep and goats in Botswana are indigenous. These animals provide income, employment and food security to the resource-poor farmers. Limited characterization of these species has been done, resulting in poor efforts to fully exploit and conserve them. The objective of this study was to phenotyically characterize indigenous sheep and goats countrywide. Measurements were collected from 2783 goats and 1282 sheep kept by traditional farmers, covering nearly all the districts of Botswana. In each district a total of 15 farmers with sheep and goats were selected randomly and records were taken on 4-12 animals per farm, depending on average district flock size. Traits recorded for each animal were body length, body weight, ear length, heart girth, height at withers, hip width, neck length, rump height, shoulder width, tail length (goats only) and horn length. Age (estimated from dentition) and sex of the animals were also recorded and vegetation type was noted. The data were analysed using the general linear model procedure in Statistical Analysis System. Prior to analyses, a main effects model of sex, age and vegetation type was fitted. Later, two types of analyses were done: (i) within a vegetation type fitting sex and age and their interaction, and (ii) within sex fitting age and vegetation type and their interaction. Least-squares means were separated using Student's t-test. Sex, age and vegetation significantly (p<0.05) affected the magnitude of traits. Phenotypic body measurements of castrates were generally higher than in both females and entire males, which were similar. The body measurements of younger animals were less than those of older age groups since the former were still growing compared to the latter. Different vegetation types promoted different body measurements, which should be expected due to differences in nutrient supply from different vegetation types. The indigenous breeds of sheep and goats can be classified as medium-size breeds. The breeds should be conserved since they are well suited to the harsh environment of Botswana where drought and livestock diseases are ever present. Efforts should be undertaken to characterize them genetically and increase their productivity.