Local mango (Mangifera indica L.) in rural Kenya are highly valued for home consumption and are perceived to exhibit greater drought tolerance and pest resistance compared to improved commercial varieties. These attributes make them promising candidates for genetic improvement and breeding programs. However, research in Kenya has largely overlooked these local varieties, focusing instead on introduced cultivars. This study presents the first comprehensive morphological and molecular characterization of 38 local mango landraces from Eastern and Central Kenya. Morphological assessment was conducted using 75 descriptors—44 qualitative and 31 quantitative—based on the Bioversity International descriptor list for mango. Hierarchical cluster analysis revealed six distinct morphological clusters, while molecular characterization using 19 simple sequence repeat (SSR) markers identified eight genetic clusters. Dendrograms constructed using Nei’s genetic distance and Neighbor Joining methods illustrated genetic relationships among the samples. Notably, four of the eight molecular clusters were congruent with morphological groupings, demonstrating partial alignment between phenotypic and genotypic classifications. The study highlights the reliability of morphological traits for field-based identification, such as in nurseries for rootstock selection, although environmental factors can influence phenotypic expression. In contrast, molecular markers provide more consistent results across conditions, making them suitable for long-term conservation and breeding. These findings underscore the need for enhanced conservation strategies, including circa situ conservation on farms and the promotion of “conservation through use” approaches. The outcomes of this research lay a critical foundation for safeguarding the genetic diversity of Kenyan mango landraces and integrating them into sustainable breeding and conservation programs.