Gao, M.-F., Peng, H.-Z., Li, S.-S., Wang, X.-L., Gao, L., Wang, M.-H., Zhao, P.-F. and Zhao, L.-X. 2015. Insight into flower diversity in Solanum lycopersicum and Solanum chilense using comparative biological approaches. Can. J. Plant Sci. 95: 467-478. Flowers, the defining feature of angiosperms, are reproductive organs that enable the continuation and propagation of flowering plant species. However, intra- and inter-species specific reproductive barriers have often evolved in plants; one such example being in the section Lycopersicum of the genus Solanum. This biological phenomenon is closely related to flower diversity, including visible morphologic features and processes such as pollination and fertilization are influenced by floral morphology, although the exact relationships remains unclear. In this study, two distinct Solanum accessions that exhibit either self-compatibility (SC) (S. lycopersicum, P86) or self-incompatibility (SI) (S. chilense, LA2405), from section Lycopersicum in Solanum were subjected to comparative analyses focusing on flower diversity. The long style of LA2405 was found to differ from that of P86 in that it exserts from the anther cone, and the irregular ‘long strip villi on the lower style of LA2405 were structurally distinct from the typical ‘finger shape’ villi of P86. Pollen grains from both LA2405 and P86 were able to germinate on their own stigmas and those of the other accessions. Pollen tube growth was arrested 1/2 and 3/4 of the way down the style in P86 and LA2405, respectively, when LA2405 was used as pistil parent. Additionally, the disappearance of starch grains and lipid bodies in the cytoplasm of the transmitting tract cells was most evident in cells that were close to the pollen tube. An analysis of the expression of flower associated genes revealed that CUL1 and SLF had an anther-specific expression pattern, while SKP1 and RBX1 were constitutively expressed in flowers of both LA2405 and P86. It was also found that transcript levels of four flower associated genes encoding subunits of the SCF complex (Skp1-Cullin1-F-box-Rbx1) were higher in anthers than in other floral organs of the flower, and higher in LA2405 than in P86. Phylogenetic analysis of CUL1 sequences and RAPD (random amplified polymorphic DNA) analysis (genome-wide scanning) indicated that flower associated genes may represent a good resource for evaluating evolutionary relationships between tomato species. Taken together the results suggest that comparative biological methods not only represent a platform for detecting evolutionary differences in flowers of different tomato species, but also provide useful data for further dissecting the mechanisms of reproductive behaviors.