With the use of parental forms of Capsicum annuum L. (Dobrynya Nikitich, Kolobok, Prometei varieties and also L 48 and L 49 lines) by the regression-cluster analysis the authors revealed the correlation between degree of identity of key alleles of economic valuable determinants and effect of heterosis. It was shown, that for the prognosis of heterosis in the conditions of the film nonheated greenhouse on module of marketable crop the degree of identity alleles in three clusters: fruit’s length—fruit’s index, fruit’s rot and duration of I phenophase—number of cameras in fruit; in the conditions of open ground — identity in the clusters: fruit’s length—fruit’s index, average fruit’s mass—marketable fruit’s mass have key significance. For the forecast of heterosis on mentioned module for both variants of growing the correlation between character and degree of identity of alleles in clusters: fruit’s length—fruit’s index and duration of II phenophase—duration of III phenophase is important.