Cariniana estrellensis and C. legalis are two of the largest trees in the Amazon and Atlantic Forest biomes that are currently vulnerable to extinction due to the intense deforestation of these biomes. Strategies for in and ex situ conservation are urgent and studies of genetic diversity and gene flow are necessary to inform such strategies. Here we investigate the historic pollen and seed flow, dispersal distance and patterns in fragmented populations of both species, using microsatellite

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... rs. All trees found in the populations were mapped, measured for diameter at breast height (DBH), and bark cambium sampled. For both species, high levels of seed (38.5-61.5%) and pollen (80.1-100%) immigration were observed, showing that populations are not genetically isolated. No self-fertilization was detected, but we did find evidence of mating among related trees (8.9-12.5%), suggesting stronger selection against selfed individuals than those originating from mating among relatives. The realized pollen and seed dispersal for both species reached long distances (C. estrellensis > 3 km, C. legalis up to 385 m), but in general followed a pattern of isolation by distance. The effective size ( e N ) in three populations (10-33) was lower than suggested for short term in situ genetic conservation ( e N < 70). For in situ conservation, the results show that the surrounding forest fragments must be preserved to maintain connectivity between the studied populations and other trees of the species and where the e N was insufficient for short term in situ genetic conservation, the e N must be increased through the introduction of at least 150 individuals.