In this study, a species inventory of terrestrial vascular plants was carried out on five islands, Dongji-yu, Sigji-yu, Dongyuping, Siyuping, and Tsuto-yu, located on the southeast of Penghu Archipelogo. A total of 44 families were recorded and could be categorized into 127 genus and 158 species. The largest island, Dongji-yu (1.54 km2), has 125 species, while the smallest island, Tsuto-yu (0.09 km2), has 29 species. Six endemic species of Taiwan were recorded in this study, including Cassia sophora L. var. penghuana Y. C. Liu et F. Y. Lu, Justicia procumbens L. var. hirsuta Yamamoto, Chamaesyce taihsiensis Chaw and Koutnik, Hedyotis taiwanense S. F.Huang & J. Murata, Chloris formosana (Honda) Keng, and Digitaria sericea (Honda) Honda. Analysis showed a significant relationship between the island’s area and the number of its species (=0.05). However, Siyuping had more species than Sigji-yu and Dongyuping even though its area was smaller than that of the other two islands. This is probably because goats were only recently introduced into Siyuping and has limited population. The similarity index of Sorensen was used to analyze the floristic relationship among the islands investigated. Results showed that adjacent islands have a close floristic relationship. However, common plant index might be more suitable for floristic relationship analysis than Sorensen similarity index, as the two islands are not comparable in size. The study also showed that coastal areas consist of more native species than inland areas in the islands, and that wetlands are rare in the arid environment of Penghu Archipelago. Thus, those habitats are especially important for vegetation conservation.