The status of native floral diversity in Mt. Manunggal, Cebu Island, the Philippines in relation to environmental factors and alien plant invasion has not been recorded and published. To assess factors influencing native plant communities in Mt. Manunggal, a vegetation survey of native and alien plants, as well as selected environmental variables at two sites (Site 1- invaded plot; Site 2- adjacent uninvaded plot) were measured, and anthropogenic disturbances observed using a t-test, regression analysis, and Pearson correlation. For each site, selected environmental parameters, as well as native and alien plant abundance and diversity, were determined last October-November, 2016. There was also a characterization of sites with respect to anthropogenic disturbances. Altitude (t= -14.11, p=0.000), soil temperature (t=2.68, p=0.014), and light intensity (t = -2.61; p=0.016) significantly differed between study sites due to the complex topography and geology of Mt. Manunggal, the variation in floral cover, and degree of anthropogenic activities. Among all environmental factors at both sites, altitude was highly positively correlated to alien plant abundance (r=0.709;p=0.000) at Site 1 while native plant abundance at Site 2 was negatively correlated with soil pH (r=-0.579;p=0.003).There was an apparent domination of alien plants in terms of species richness and abundance at both sites and this could have significantly affected native plant abundance. The strong correlation of environmental parameters to alien plant invasion could favor the continued dominance of alien plant species, resulting in a further decrease of native species.