Both the continental or island origin of Hainan, and the Indo-Malaysian or East Asian affinity of its flora, are debatable. In this study, 196 families, 1283 genera and 3894 species of Hainan plants were recognized. Patterns of seed plant distribution were quantified at the generic and the family levels. The floras of Vietnam, and the adjacent Guangxi and Guangdong provinces of mainland China, were compared with Hainan. The results showed that the flora of Hainan Island is dominated by families and genera with tropical distributions. Among its floristic elements, tropical Asian distributions make up 23.85% of the total flora, while East Asian distributions contribute only 3.74%. There are only 7 genera and c. 10% of species endemic to Hainan Island. The Hainan flora has strong similarities to the flora of Vietnam at the family and the generic levels, and also to the flora of Guangxi, but less with the adjacent Guangdong province. The main conclusions are: Hainan’s flora is tropical in nature with a strongly tropical Asian affinity, and it has very low endemism at the generic and species levels, which implies a continental origin. We conjecture that Hainan Island could have been adjacent to northern Vietnam and the Guangxi at least in Eocene. This suggestion is supported by palaeobotanical, palaeomagnetic and volcanism studies.