Island-endemic arthropods are understudied species and likely to be highly threatened with extinction. Analysis of IUCN Red List assessments can be used to highlight important microhabitats requiring conservation for the effective management of island-endemic arthropod biodiversity. We synthesized information on the 296 island-endemic arthropod species assessed as Critically Endangered as of April 2024, the geography of the islands to which they are endemic, and the broad threats they face. These species comprised 33 taxonomic orders, across which an average of 53% of species were limited entirely to tiny, confined areas of habitat: caves, high elevation areas, isolated pools or sea stacks. These micro-refugia are most utilized by crustaceans and least utilized by myriapods. Caves and pools are the most important habitats on temperate islands where habitat degradation threatens crustaceans. On small tropical islands where arachnids and hexapods are threatened by invasive species, refugia are mostly in high elevation areas. Sea stacks appear to be effective refugia from invasive species only for threatened island-endemics with notable long-distance dispersal adaptation. None of the refugia appear effective in sustaining arthropod species immediately threatened by climate change. Using the interaction between arthropod life history, habitat and threats, it is possible to generalize micro-refugia that (1) should be immediately targeted for management, and (2) could yield undescribed or presumed-extinct species. Prioritizing such refugia for management and research can guide efficient expenditure of local capacity. In our case study, on Ascension Island, micro-refugia for seven endemic arthropods covered < 0.1% of the island's total area.