Tomato (Solanum lycopersicum L.), is an economic plant which belongs to Family Solanaceae and is widely consumed as food and other processed natural products. Tomato production areas are faced with economic losses due to early blight disease caused by Alternaria solani. Early blight disease reduce yield and renders fruit unmarketable, Cultural practices and fungicides are majorly adopted in the management of this disease. The use of tolerant varieties and Glomus clarum as alternatives which are environmental friendly necessitated this study. Therefore, this study investigated genetic resistance of tomato to early blight disease using Glomus clarum as revealed by SSR marker . Eight tomato accessions obtained from NACGRAB and Technoserve were evaluated, while Ojoo market accession served as check. The experimental treatments Control, Glomus clarum + Pathogen and Pathogen only were laid out in a complete randomized design with three replicates. The result showed that Rukuta Jubia and NGB00727 accessions had the highest mean values for stem girth (0.59cm) and leaf width (3.74cm) respectively, while Ojoo Market performed best for leaf length (6.78cm). Glomus clarum significantly (p˂0.05) influenced the resistance of NGB00727 to Alternaria  solani ,and enhanced the production of flowers (2.53) and  mean weight of  fruit per plant (0.94g). The NGB00727 accession showed the highest resistance to early blight disease, while NGB00754 accession was the most susceptible to Alternaria solani.