In less than four decades from now Africa must feed an additional 1.3 billion people. Due to this rapid population growth and increasing rate of urbanisation, Africa’s demand for wheat is greater than for any other food crop. Wheat will therefore play a critical role in ensuring food and nutritional security in Africa. However, wheat production in Africa is currently characterised by low yields, high susceptibility to biotic and abiotic stresses, and poor end-use quality partly attributed to the use of poor quality seed with low genetic potential. To determine the gene pool currently exploited for wheat improvement in East Africa, we examined the allele diversity of 35 functional genes in a collection of 250 wheat landraces, cultivar and breeding lines from Kenya and Ethiopia using previously validated KASP assays. The assayed genes control or are linked to various economically important traits including plant height (PH), thousand kernel weight (TKW), grain protein content (GPC), Pre-harvest sprouting (PHS), yellow rust (YR), leaf rust (LR) and stem rust (SR) resistance. The results revealed low frequencies of beneficial alleles of some major genes in this population including Rht-D1 (9%) for reduced PH, GPC-B1 (2%) for increased GPC, TaSdr1 (13%) for reduced PHS sprouting resistance, and Yr5 (0%)and Yr15 (7%) with effective broad-spectrum resistance to multiple races of YR. Furthermore, we found that allelic variation in TaCKX-6A accounts for 25% of the variation in grain weight in Ethiopian germplasm under field conditions but is only present in less than 15% of the East African wheat germplasm. Together these results uncover hitherto unexploited gene pool that can be used to improve the genetic potential of the East African wheat germplasm. We present a proposal to rapidly mobilise these beneficial alleles into a common adaptable East Africa wheat background.