Abstract This study tested the hypothesis that self‐compatibility would be associated with floral traits that facilitate autonomous self‐pollination to ensure reproduction under low pollinator visitation. In a comparison of two pairs of Ipomoea species with contrasting breeding systems, we predicted that self‐compatible (SC) species would have smaller, less variable flowers, reduced herkogamy, lower pollinator visitation and higher reproductive success than their self‐incompatible (SI) congeners. We studied sympatric species pairs, I. hederacea (SC)– I. mitchellae (SI) and I. purpurea (SC)–I. indica (SI), in Mexico, over two years. We quantified variation in floral traits and nectar production, documented pollinator visitation, and determined natural fruit and seed set. Hand‐pollination and bagging experiments were conducted to determine potential for autonomous self‐pollination and apomixis. Self‐compatible Ipomoea species had smaller flowers and lower nectar production than SI species; however, floral variation and integration did not vary according to breeding system. Bees were primary pollinators of all species, but visitation rates were seven times lower in SC than SI species. SC species had a high capacity for autonomous self‐pollination due to reduced herkogamy at the highest anther levels. Self‐compatible species had two to six times higher fruit set than SI species. Results generally support the hypothesis that self‐compatibility and autonomous self‐pollination ensure reproduction under low pollinator visitation. However, high variation in morphological traits of SC Ipomoea species suggests they maintain variation through outcrossing. Furthermore, reduced herkogamy was associated with high potential for autonomous self‐pollination, providing a reproductive advantage that possibly underlies transitions to self‐compatibility in Ipomoea.