Habanero peppers have become increasingly popular in the United States for supplying unique flavors and high levels of pungency. As consumption of this product increases, development of improved cultivars with elevated phytochemicals will likely result in additional demand from consumers. This study evaluated fruit size, capsaicinoid, and flavonoid concentrations in six Habanero (Capsicum chinense) genotypes grown at three different Texas locations: College Station, Uvalde, and Weslaco. Five of these Habanero experimental hybrids (H1-red, H2-orange, H3-orange, H5-dark orange, and H6-yellow) were developed at Texas A&M University with genetic improvement in numerous traits of interest, and Kukulkan F1 (Kuk-orange) was included as a commercial control. In general, H1-red had the largest fruits in these locations. Capsaicin and dihydrocapsaicin (DHC) concentrations were highest in Kuk-orange followed closely by H5-dark orange and were lowest in H6-yellow. Fruit at Weslaco was larger and contained more capsaicin and DHC than those produced in Uvalde or College Station. Although flavonoid contents were variable and low in all genotypes and locations, H3-orange showed the most stability for use in future crossing schemes to compete against Kuk-orange for this characteristic. Our results suggest that variation in phytochemicals in fruit tissue of Habanero genotypes can be exploited by selecting in an appropriate environment.