Invasive alien species are one of the most severe threats to island biodiversity. An essential first step in addressing this issue is producing comprehensive inventories of alien species inhabiting them. However, cataloguing alien floras on remote islands is particularly challenging. Botanical surveys are often conducted only after substantial human-driven impacts on local ecosystems, including the introduction of invasive species, have already occurred. This raises the key question of how species' native origin should be determined on islands with such a recent history of botanical documentation. Site-based methodologies offer a practical, replicable and context-sensitive approach to addressing these challenging knowledge gaps. Here, we present a comprehensive catalogue of the alien spermatophyte flora of Isla del Coco, an eastern Pacific island located approximately 500 km off the Central American mainland and facing the aforementioned challenges. Among the main contributions of this study, we apply an expert-based binary decision tree to classify the wild flora as native, wild alien, or cryptogenic, along with a separate inventory of cultivated species. Our classification system allowed us to identify 89 wild alien species (45.2% of the island's total wild flora), 78 native species (39.6%), and 30 cryptogenic (15.2%). The naturalised-to-native ratio (0.5) suggests that the island remains highly susceptible to biological invasions. The profile of the alien flora closely resembles that of mainland Central America, with a predominance of unintentionally introduced species, underscoring the need for strict biosecurity measures at landing points. The methodology employed also indicates that site-based approaches may apply stricter criteria for defining native species than previous studies, thereby highlighting new research needs for Isla del Coco, such as clarifying the status of cryptogenic species and investigating the largely unexplored impacts of invasive alien plants.