Context: Continental islands are important conservation targets because of their ecological singularities. In the Mexican Pacific, the Chamela Bay Islands Sanctuary in the state of Jalisco is little or not studied at all in terms of biodiversity. Aims: The aim of this study is to contribute to the management plan of the sanctuary by presenting a detailed analysis of native vegetation surveys of three islands of the sanctuary. Methods: We used quadrats and treks to record and compare plant diversity, species richness, and structure of woody and cacti vegetation of the islands of Cocinas, La Pajarera, and San Agustín. Key results: There are 42 woody and seven cacti species on the three islands (Cocinas 28, La Pajarera 17, San Agustín 30), which represent 9% and 42% of the woody and cacti species recorded regionally, respectively. The islands harbour 20 endemic Mexican species (regionally, 8.6% of woody and 30% of cacti species) and four species in some threatened category (regionally, 0.4%). Plant species richness and vegetation structure differ among the three islands, which shared only seven species. Conclusions: The richness and abundance of woody and cacti species on the three islands (total area: 55.5 ha) that include Mexican endemic and threatened species emphasise the importance of protecting the whole islands. Implications: The islands need a more active vigilance to avoid induced fires and vegetation removal. Our results point out these factors as the major threats for the islands' conservation. Three protected islands with the same geological origin on the Pacific Coast, in Jalisco, Mexico, differ in species richness and habitat structure, sharing only 7 of 49 woody and cacti species. Observations suggest that human disturbances are threatening the maintenance of their diversity. The islands need an effective biodiversity monitoring and conservation program because they represent unique habitats. [ABSTRACT FROM AUTHOR]