Iriartea deltoidea (Arecaceae) is an abundant canopy palm with a wide geographic distribution in Neotropical wet forests. We analyzed the genetic profile across three generations of Iriartea within a 43-ha area encompassing two areas of second-growth and adjoining old-growth forest at La Selva Biological Field Station in northeastern Costa Rica. A total of 311 reproductively mature trees, 99 large saplings, 207 small saplings, and 601 seedlings were genotyped using 141 AFLP loci. Parentage analysis revealed high dispersal distances, both for seed (over 2.3 km) and pollen (over 3.8 km), indicating a large genetic neighborhood within La Selva Biological Station. In a 20-ha area of second growth, the founding palm population was dominated by a small number of parental trees located in the adjacent old-growth forest; two old-growth trees contributed 48% of the second-growth genes. The genetic diversity of reproductively mature trees in this second-growth forest was significantly reduced compared to adjacent old-growth forest. Within 400 m of the border with old-growth forest, we observed a similar reduction of genetic diversity in saplings, and an even greater loss of genetic diversity in the second generation of seedlings. Nearly half of these seedlings were offspring of local parents. In contrast, in the distant portion of second-growth forest (400–800 m from the old-growth border), parentage analysis showed that 40% of seedlings originated from outside the study area and only 10% were offspring of local parents. These high levels of gene flow maintained genetic diversity in saplings and seedlings similar to levels observed in old-growth forest. Our findings highlight the importance of gene flow from diverse seed and pollen sources for sustaining levels of genetic diversity of tree populations in second-growth forests.