This work reports on the fruit surface and anatomy of seven Neotropical species of Indigofera (I. campestris Bong. ex Benth., I. hirsuta L., I. lespedeziodes Kunth, I. microcarpa Desv., I. spicata Forssk., I. suffruticosa Mill., and I. truxillensis Kunth) to help species diagnosis and clarify the fruit type classification. Flowers and fruits at several stages of development were removed from living material, fixed, and examined with scanning electron (surface analyses) and light microscopies (histological analyses). Species showed differences in relation to the number of exocarp layers, secretory trichome morphology and distribution, presence of stomata, phenolic idioblast size and distribution in mesocarp, the number and arrangement of endocarp fibers, and the presence of a separation tissue. It is noteworthy that no separation tissue was observed in I. microcarpa and I. suffruticosa, although they have dehiscent fruits, which indicates a delayed dehiscence. The present work confirms that fruit anatomical characters can be utilized as a tool for fruit type classification, especially in Indigofera, the third largest genus of Leguminosae.