Inheritance of fruit-related traits was studied in a population generated by crossing two heirloom pepper (Capsicum annuum) cultivars, Round of Hungary and Bulgarian carrot. Inheritance of corrugated pericarp phenotype of ‘Round of Hungary’ behaved as a recessive trait controlled by two genes while round fruit shape behaved as a single gene. Pungent cultivar Bulgarian carrot had significantly higher total soluble solids, titratable acidity, antioxidant activities, and significantly thinner pericarp than fruit of Round of Hungary. Pericarp thickness was related to differences in both cell number and cell size. Analyses of F2 fruit indicated that fruit weight was positively correlated (P < 0.01) to fruit width and pericarp thickness. Fruit width was negatively correlated (P < 0.01) to fruit length and total soluble solids and positively correlated (P < 0.01) to pericarp thickness. Yellow color was negatively correlated (P < 0.05) to total soluble solids. Fruit length showed high inbreeding depression and transgressive segregation. Color measurements showed that yellow was correlated to lightness, and the relationships between red and yellow color spaces and carotenoid composition were complex.