Cowpea (Vigna unguiculata L. Walp) is an important grain legume in East Africa and isrnmainly grown by small-scale farmers. Drought tolerance, early maturity, nitrogen jixation,rnand loll' fertility requirement are important characteristics for adaptation to the (by regionsrnof Sub-Saharan Aji-ica. COll1Jea is a multijunctional crop providingfood to both humans andrnanimals. Because it is rich in protein, cowpea is a cheap source of protein for resourcelimitedrnfamilies in Sub-Saharan AjiÂ·ica. Understanding the genetic diversity in cowpea is arncrucial initial step towards planning a comprehensive conservation and cowpea improvementrnstrategy. Little or no study has been conducted to understand the diversity and relatedness ofrnCOllpea germplasm in East Aji'ica, particularly in Ethiopia. This PhD research jirstrninvestigated patterns of molecular diversity among 210 accessions of Ethiopian local COllpearnof cowpea using 23 microsatellite markers (SSR). Additionally, the levels of genetic diversityrnof 95 COllpea accessions from East Aji'ica and inbred lines ji-OI1l llTA were assessed using arnset of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNP~). The averagerngenetic diversity (D), as quantified by the expected heterozygosity, was 0.47. A total of 75rnalleles with the average number of 3 alleles pel' locus were recorded and two rare allelesrnwere registered when screened with SSRI marker. The mean polymol1Jhic informationrncontent was 0.4. The accessions were not grouped according to their geographical origins.rnThree main cluster groups were identifie(l, and the sub-groups identified by neighbor joiningrnwere in accordance to the clusters revealed by the structure analysis. The AMOVA resultrnshowed moderate differentiation among populations (Fst ~ 0.075) and high genejiow (Nm ~rn3.176) between and among regions; indicating that there was significant germ plasmrnexchange between the regions considered. The accessions in this study possess wide diversityrnwithin both individuals and populations. The study also detected five promising Ethiopianrnaccessions ji'om 'Amhara', 'Gambella' and SNNP regions, tightly clustered and sharing arncommon allele with the multi-race striga resistant accession B301ji'om Botswana, whichrncould help in identification of appropriate parental lines among Ethiopian accessions ofrncOllpeafor Striga gesnerioides resistance. The rare alleles identified were linked to desirablerntrait of striga resistance against Striga gesnerioides, SG3, RACE. The SSR markers tested inrnthis study can thus be used for analyzing cOllpea diversity reliably The polymorphicrninformation col1lent (PIC) value was IIlOre than that of some Aji'ican countries, Ghana,rnSenegal and Kenya; however, considerably lower than that of the wild cOllpea types;rniiirnorntherifore, the results obtained in the present study reinforce the need to protect alld conservernvaluable genetic resources and the finding also showed that the genetic base of Ethiopianrncowpea is narrow. Regarding the comparative study of accessions from some of East Aji-icanrncountries and lITA inbred lines of cowpea, the result showed that the average geneticrndiversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52)rnthan for SNPs (0.34). The average number of alleles per locus was higher for the SSRrnmarkers (6) than for the SNP (2) markers. The PIC was 0.48 for SSRs and 0.28 for SNPsrnwhile the fixation index was 0.095 for SSRs and 0.15 for SNPs showing moderaterndifferentiation and high gene fiow among East AjNcan countries; and thus the existence ofrngerm plasm exchange among the East AjNcan countries. The cluster analysis showed arnsimilar pattei'll for both SSR and SNP markers detecting a substantial degree of associationrnbetween origin and genotype. However, some accessions }i'om different regions clusteredrntogether. The geographic distance and the genetic background of the accessions were notrnclearly refiected in the accession clustering of genetic tree constriction and principalrncomponent analysis. The results of fixation index, neighbor joining and genot)qJe clusteringrnagreed in both SNP and SSR markers. Thus for the assignment of genotypes to subgroupsrnboth neighbor joining and PCoA clustering methods are equally appropriate. Thernpolymorphic information content (PIC) value of all of the east AjNcan countries were morernthan some of west AjNcan countries, Ghana and Senegal but noticeably lower than the wildrncOlllJea types. Therefore, the results obtained in the present study showed that the cowpearngenetic base of Ethiopian and other East Aji'ican countries is narrow. It is recommended thatrnthe narrow genetic base can be augmented through introduction of accessions with desirablernalleles. Since the study showed that /IIost of the accessions }i'om the gene bank are a mixturernof sub-accessions Ethiopian Biodiversity Institute (EBl) should consider reorganizing theirrnseed stock by taking the subtypes identified in this study into account.rnKeywords: Cowpea, Genetic diversity, SSR, SNP, Ethiopia, Kenya, Somalia, Sudan, inbredrnline, East Africa, germplasm