Species co-occurrence has been widely used to infer ecological and evolutionary processes underlying biodiversity patterns. The most studies have focused on species co-occurrence within a local community or assemblage (i.e. site-based approach). Because an species co-occurrence in a site is an instance of possible co-occurrence patterns, site-based approach may fail to detect the non-random processes underlying co-occurrence pattern. As an alternative approach, we can characterize species by all congeneric species within their distribution ranges. This enables comprehensive evaluation of species co-occurrence and may be a promising tool for inferring eco-evolutionary background of species co-occurrence. I will introduce a case study for examining co-occurrence patterns between native and exotic plants in the East Asian Islands. Then, I will discuss potential mechanisms of naturalization success, with highlighting the advantages of the species-based approach.