There are four ostrich subspecies classified under Struthio camelus. The Somali ostrich (Struthio  molybdophanes) is highly differentiated from the four subspecies and it has recently been recognised as a separate species. Within Eastern Africa, a drastic decline in population of the new species has been reported in its’ Somalia range. The only other important range of the species that could be targeted for conservation is Samburu, Kenya. In this range, indirect threats to the survival of the Somali ostrich may be occurring through habitat loss and fragmentation. The magnitude and consequences of these threats to its’ genetic diversity has not been established. We investigated the genetic diversity of the Somali ostrich in Samburu national reserve, Maibei and West Gate Conservancies of Samburu, Kenya using microsatellite markers. The microsatellite markers we used were highly polymorphic and can be used in genetic analysis of S. molybdophanes. We found low levels of genetic diversity in the three ostrich populations. The ostrich population in Samburu national reserve had the highest number of private alleles indicating that this population is genetically distinct. Our results also show that the genetic diversity of the Somali ostrich in Samburu is very low compared to other ostrich subspecies and this may result in reduced fitness and inability to adapt to changing environmental conditions in the long term. Based on these findings we recommend collaboration between conservation partners and Samburu community in conserving Somali ostrich within Samburu community conservancies. This calls for awareness campaigns and outreach programs that will enhance capacity of Samburu community in conservation approaches.