The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito' groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.