Field surveys along the Lake Basin and the Coastal regions of Kenya were carried out to assess the natural incidence of pathogenic microorganisms associated with the legume pod-borer, Maruca testulalis Geyer on the cowpea crop. A regular sampling regime was maintained on plots planted with four varieties of cowpea: T VX 66–2H, Vita 3 (TVU 1190), Ex-Luanda and Nyar-Milambo. Larvae of M. testulalis were recovered from the flowers and pods of the crop, and subjected to routine laboratory disease diagnosis including: tissue examination, culture incubation, microscopy and pathogen identification. The main groups of pathogenic microorganisms found to act as natural mortality factors to M. testulalis larvae include: protozoa, bacteria, fungi and a virus. A higher level of disease incidence and diversity on M. testulalis larvae occurred in the lake basin region of Kenya than the coastal part.