A fast and accurate genetic purity test of F1 hybrid plants is essential for seed production and accelerating advanced breeding generations in breeding programmes. DNA technology has great potential for enhancing purity assessment of hybrids. Genetic purity of three F1 chili hybrids was determined using two molecular marker techniques RAPD and ISSR. RAPD analysis successfully detected all three F1 hybridity, while ISSR detected only two. This was due to the RAPD marker system producing a greater number of markers than the ISSR system.