This study analysed the anatomical structure of the seed coats, identified the location of water uptake and evaluated the effects of alternating temperatures and heat treatment on the breaking of physical dormancy of two species of Fabaceae (Caesalpinioideae), Cassia leptophylla and Senna macranthera, from the Atlantic forest of Brazil. The seed coats of both species consisted of a cuticle (extra-hilar region) or remaining funicle region (hilar region), subcuticular layer, palisade layer with lignin, osteosclereids, sclerified parenchyma and white cells. The palisade layer was formed by elongated macrosclereids with a light line of callose. In thermally scarified seeds of C. leptophylla, water entered through the micropylar canal, and in S. macranthera the water entered through the lens. Alternating temperatures that ranged from 15 to 30°C did not break physical dormancy of either species; however, exposure to 50°C broke seed hardcoatedness, allowing the entrance of water in both species.