Six Egyptian new hybrids belonging to two species of Capsicum L. were analyzed using biochemical markers. Low polymorphism percentage (38%) was recorded in the SDS-PAGE pattern. Two species-specific, one for each species, were scored and could be used as biochemical markers. Eight-isozyme systems produced 21 bands, among them only three patterns; alcohol dehydrogenase, malic enzyme and malate dehydrogenase, recorded polymorphism percentages ranged between 57 to 80%. Five characterized unique bands were detected; two in yoser 4 of C. frutescens and three in kotof 2 of C. annuum. The UPGMA dendrogram revealed low genetic variability of the six hybrids that separated into two main clusters with genetic distance of 0.25.