The sky islands of the Chihuahuan Archipelago are montane isolated systems surrounded by the Chihuahuan Desert. Despite their relevance for conservation, floristic diversity patterns are misunderstood. This study characterized the floristic diversity within the 54 sky islands from species occurrence records. Moreover, geographical patterns of species richness, endemism, micro-endemism, extinction risk, human influence, land cover change, and protected land were criteria to identify the priority sky islands for conservation. Within the Chihuahuan Archipelago, 135 families, 731 genera, and 2,244 species were recorded, of which 296 were endemic, 95 were micro-endemic, and 45 were threatened. The xeric shrubland hosted the highest species richness, endemic, micro-endemic, and threatened species. The most representative families were Asteraceae, Poaceae, and Fabaceae. Chisos, Davis, and Glass were the sky islands that hosted the most species richness, each above 770 species. Most endemic and micro-endemic species were found in Chisos, La Fragua, La Madera, La Paila, and Roque. Meanwhile, most threatened species were found in La Encantada, La Paila, La Vega, Maderas del Carmen, and San Francisco Desmontes. Moreover, human influence was low in 80% of the sky islands. Davis, Organ, and Glass experienced high land cover change, whereas 30% of the sky island surface was protected. The priority sky islands were Big Bend, Chinati, Chisos, Davis, Glass, Franklin, La Encantada, La Gavia, La Madera, La Paila, La Vega, Las Delicias, Maderas del Carmen, Organ, Roque, and San Francisco Desmontes. Our findings are crucial to inform strategies to conserve the floristic diversity in the Chihuahuan Archipelago.