Human activities, such as agricultural activity, housing construction, forest logging, etc., play an important role in vegetation changes. Any disturbance to the ecosystem by a severe change in landscape patterns may reduce the survival capacity of certain plant species. In recent years, many studies have used a geographic information system to establish spatial data on vegetation changes; this information includes both the plant species and their spatial structure. Therefore, the aim of this study is to investigate the trends and patterns of vegetation changes and the degree of correlation with the particular environmental features at Wangan Island and Chimei Island in the Penghu Islands, from 1979 to 2009. Both islands have very similar natural features, including geographic location, natural environment, and economic development, but the spatial structures of the land use type are different. The study makes use of geographic information systems, detrended correspondence analysis, canonical correspondence analysis and landscape ecological indicators as study tools. The results are expected to promote our understanding of the spatial distribution patterns of vegetation types and plant species. The results can be divided into three areas. First, both islands follow the same trend with regard to changes in land cover, but the rates of change are different. And the spatial structure of land use types affects the location of land cover types. Example, the centralized and decentralized villages both impact the distribution of the woodland. The mesh and ring road both impact the location of agricultural land. Second, the grassland plant species are correlated with the environmental factors, but the forest plant species are not. The major woodland specie is Leucaena leucocephala on both islands, whose physiological habits may reduce the degree of the correlation. Third, compared to the two islands, Chimei Island is more significant about that the vegetation types are correlated with the neighboring land use types. Finally, the plant species of the local vegetation types could be predicted by changes in the type of land use. In addition, this study has built a trend scheme of the spatial structure changes on Wangan Island and on Chimei Island, which can be used in the island¡¦s future environmental planning.