Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current-day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers.We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep-water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long-term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate-induced refugia acted in concert to produce great species diversity and endemism in the Philippines.