Most extinctions worldwide have occurred on islands, primarily due to interactions with exotic species, but rarely due to interactions among endemic species. This potential exists on two of the California Channel Islands, Santa Cruz and Santa Rosa, as endemic island spotted skunks (Spilogale gracilis amphiala) appear to have rapidly declined to rarity, possibly due to interference competition with endemic island foxes (Urocyon littoralis). Niche partitioning is expected in response to interference competition; hence, it is surprising that skunks and foxes show extensive overlap in macrohabitat use and circadian activity. However, the role of microhabitat associations and fine-scale temporal activity in facilitating coexistence of the two species has not been explored. We evaluated microhabitat associations of island spotted skunks and island foxes across both islands using data from live traps and wildlife cameras collected during 2015–2017, and we analyzed fine-scale temporal activity using camera data from 2016 and 2017. On both islands, skunks had a positive response to ground-level cover provided by rugged topography or woody vegetation such as shrubs or trees, whereas foxes had a weak or negative response, suggesting partitioning of these microhabitat characteristics. Additionally, on both islands the peak in timing of skunk activity offset the peak for foxes, which implies that skunks use fine-scale adjustments in activity to avoid foxes. Past grazing by exotic herbivores likely reduced habitat refuges for skunks; however, as vegetation on both islands recovers, regrowth of shrubs and trees may provide cover that will improve prospects for coexistence of island spotted skunks and island foxes.