Abstract Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval ( GI ) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders ( fa/fe ) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size ( Ne ) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.