Seed-borne fungi cause several diseases of common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.). The survey of seed-borne fungi of common bean and soybean was carried out on three  Egyptian Governorates (Behera, Dakahlia, and Ismailia) in Egypt. Nineteen fungal species comprising therteen genera were isolated from the collected common bean and soybean seed samples, using standard blotter i,e. Alternaria alternata, Alternaria spp., Aspergillus niger, Aspergillus ochraceous, Aspergillus flavus, Botryodiplodia sp., Cladosporium sp., Colletotrichum lindemuthianum, Colletotrichum dematium, Fusarium solani, Fusarium moniliforme, Fusarum oxysporum, Macrophomina  phaseolina, Myrothecium sp., Penicillium spp, Rhizoctonia solani, Stemphylium spp., Trichoderma  spp. and Trichothecium sp.  Pathogenicity tests proved that C. lindemuthianum and C. dematium were pathogenic to common bean and soybean. Polymerase chain reaction (PCR) has many beneficial characteristics that make it highly applicable for detecting Colletotrichum spp. of seeds. PCR diagnosis method and DNA extraction considered one of the most important steps and purity of DNA template for successful PCR assay. For the PCR amplification of C. lindemuthianum and C. dematium, two primers ClF4  and ClF5, stander blotter, agar plate, and deep freezing method were used as seed healthy testing methods. Stander blotter was proved the past and quickly method to detect seed-born of C. lindemuthianum and C. dematium. Trichoderma harzianum reduced linear growth for C. lindemuthianum and C. dematium followed by Trichoderma viride and Bacillus subtilis recording (3.3 cm and 3.9 cm, respectively) followed by Pseudomonas floursence  that display a high linear growth (7.4 cm). On the other hand, fungicide Aetro 30% (Iprodione + Tebuconazole) recorded the least linear growth (0.9 cm) for C. lindemuthianum and C. dematium compared with negative control recorded (9.0 cm in diameter). Thymus plant extract caused the lowest liner growth (3.7 cm). Plant extract  concentrations caused a significant reduction in the growth of C. lindemuthianum and C. dematium. The highest concentration (1.5 %) gave less fungal growth while the lowest one (0.5%) showed the highest fungal growth compared with negative control.