Community assembly of island plants is a central topic in island biogeography. Most previous studies have focused on seed plants, while our understanding of bryophytes is limited. Specifically, how dispersal limitation and habitat heterogeneity shape beta diversity of bryophyte communities on islands remains unknown. We used two datasets of bryophyte communities from an artificial (~60 yr of isolation) and natural archipelago (~8500 yr of isolation) to understand their beta diversity patterns. The null model, in which species could disperse randomly and colonize successfully between islands, but the number of species on each island and the frequency of each species occurrence across all islands remain unchanged, was used to calculate expected beta diversity. Although we found significant differences in species composition between the two archipelagos, the difference in observed beta diversity was negligible. Further, there was no significant difference between observed and expected beta diversity in each archipelago. The difference in island area, rather than isolation, was significantly correlated with the beta diversity of bryophytes in both archipelagos. Our results suggest that the dispersal limitation is not the major ecological process driving the assembly of bryophyte communities in both archipelagos, but the habitat heterogeneity related to island area determines the beta diversity of bryophytes.