fs3.1 is a major fruit shape (defined as the ratio of fruit length to fruit width) quantitative trait locus (QTL) originally detected in an intraspecific cross of Capsicum annuum between the blocky and elongated-fruited inbreds. 'Maor' and 'Perennial', respectively. In addition to increasing fruit shape index, the 'Perennial' allele at fs3.1 increased fruit elongation and decreased fruit width and pericarp thickness. We verified the effect of fs3.1 in backcross inbred lines (BILs) derived from crossing 'Perennial' with 'Maor' and with a second blocky-type inbred line of C. annuum. To determine the effect of the fs3.1 region in additional Capsicum species, we constructed an advanced backcross population from the cross of 'Maor' and the oval-fruited Capsicum frutescens BG 2816 and an F-2 of the introgression line IL 152 that contains an introgression of the fs3.1 region from Capsicum chinense PI 152225. QTLs for fruit shape, fruit width, and pericarp thickness, but not for fruit length, were detected in both crosses, indicating the conservation of the fs3.1 region as a QTL affecting fruit shape in pepper. We also tested tomato (Lycopersicon spp.) introgression lines containing the corresponding fs3.1 region from L. pennellii and L. hirsutum, but we did not detect a significant fruit shape QTL in these lines. The effect of fs3.1 on the growth of fruit dimensions varied with the genetic background. By measuring the length and width of ovaries and fruits of near-isogenic C. annuum lines that differ in fS3.1 during fruit development, we determined that fs3.1 controls shape predominantly by increasing the growth rate of the longitudinal axis in the first 2 weeks after pollination. However, in the crosses of C. annuum with C. frutescens and C. chinense, fs3.1 predominantly exerted its effect on the width dimension.