Chili (Capsicum annuum L.) is the fruit of plants, the Chili is susceptible for several diseases and seed borne fungi Phytophthora capsici which produces collar rot and root of chili. Seed borne pathogens are associated with untreated seeds of chili which are also significantly reduced the germination of seed. This experiment was conducted to find out the seed borne fungi and enhanced the germination of chili (Capsicum annuum) with two fungicides known as Mancozeb 80% WP and Carbendazim 50% WP. Effectiveness of these two fungicides were measured when the seeds planted on blotter paper in petri plates at 270C under lab conditions. These two fungicides significantly reduce the effect of seed borne fungi associated with chili seeds. Mancozeb 80% WP was found most effective to reduce the effect of seed borne fungi and increase the seed germination. Considering the results of the experiment, Mancozeb 80% WP was noted to be a best fungicide against the seed borne fungi. Keywords: Capsicum annuum, Mancozeb, Carbendazim, seed borne fungi, blotter paper. DOI: 10.7176/JBAH/10-4-04 Publication date: February 29th 2020