Tswana goats that were kept in communal systems in three agro-ecological regions in Botswana were characterized according to phenotypic measurements and genotypic data. Objective measurements for 123 goats included bodyweight (BW), body length (BL), heart girth (HG), height at withers (HW), and tail length (TL), while qualitative traits included coat colour and presence or absence of horns and beards. Age was estimated based on dentition. Hair samples were collected from 48 of the phenotyped animals in the largest region (central region) and genotyped with the Illumina Goat50K SNP chip. Mixed coat colour was predominant and across regions 95% of the goats were horned and bearded. Goats in the northwest region had the lowest BW and significantly higher HG values in all age groups compared with other regions. Goats over four years old in the central and northwest regions were significantly longer in body compared with the ones from the southern region. The average expected heterozygosity and inbreeding coefficient were 0.423 ± 0.03 and 0.009 ± 0.05, respectively. Principal component analysis clustered most animals, with a few outliers. The effective population size has decreased over time and at 13 generations ago was estimated at 266. There were high genetic and phenotypic variations in the indigenous Tswana goats, which should be exploited to increase performance through within-breed selection and structured crossbreeding.