Cape gooseberry (Physalis peruviana L.) is a neglected high potential crop, knowledge of the genetic diversity of the genotypes domesticated in Kenya is limited. To understand the genetic diversity and structure within and between Cape gooseberry germplasm, 70 accessions from six selected counties were analyzed using 15 pairs of highly polymorphic SSR primers. In this study, a total of 61 polymorphic SSR alleles were identified with mean polymorphic information content (PIC) of 0.43. Analysis of Molecular Variance (AMOVA) revealed that 92.8% of the total genetic variation was within accessions whereas variation among accessions accounted for 7.2% of the total genetic variation. Genetic diversity parameters among the 70 accessions revealed that Cape gooseberry was more diverse than previously recorded. Based on the SSR data, the 70 accessions were classified into five main phylogenetic groups, which corresponded to the county of origin through factorial analysis, principal component analysis (PCA), and phylogenetic analysis. Seven core SSR primer pairs, namely SSR1, SSR2, SSR10, SSR11, SSR123, SSR138, and SSR146 were found to have a wide applicability in genotype identification of cape gooseberry, and thus they are recommended for use in genetic characterization of germplasm collected from other counties not covered by the present study. This study demonstrated the existence of considerable genetic diversity in Cape gooseberry accessions growing in selected counties in Kenya and can therefore be used as a basis for future breeding programs in the development of hybrids with desirable traits. This wider genetic diversity is vital for posterity as it will help cope with unpredictable climatic changes and human needs.