To gain insight into the ecological processes driving community reassembly in disturbed ecosystems, we assessed the phylogenetic dispersion of early- and late-successional tree species occurring in lowland forests of northeastern Costa Rica. Early-successional species were more closely related than expected by chance, whereas late-successional species tended to be less closely related than expected by chance. Then, we evaluated temporal changes in the phylogenetic structure of seedling and tree assemblages in four 1-ha plots of secondary forests in this region. We found an increase in the phylogenetic evenness among tree individuals over time in all secondary tree assemblages, indicating that relatedness among tree individuals decreases as succession unfolds. This pattern was jointly promoted by recruitment and mortality processes, suggesting that increasing evenness was caused by the replacement of individuals of early-successional species from closely related lineages by late-successional species belonging to a wider diversity of lineages. Based on species occurrence, however, tree community reassembly did not show any significant phylogenetic trend over time. These results suggest that shifts in species abundance over succession have a greater impact on the phylogenetic structure of the community than the turnover of species. Seedling assemblages showed higher phylogenetic evenness than tree assemblages, suggesting that propagule colonization is an important process driving phylogenetic changes in species composition throughout succession. Overall, our findings showed that the phylogenetic structure of these successional communities varies at two temporal scales. At short timescales, decreased dominance by early-successional species over succession leads to increased evenness among tree individuals. At longer timescales, colonization processes result in increased phylogenetic evenness in seedling communities compared to tree communities, forecasting increasing phylogenetic evenness among adult individuals at late-successional stages.