The recent foraminiferal fauna and associated microbiota of Clipperton Island (10.2833°N, 109.2167°W) were investigated at 20 sites collected in the intertidal zone around the perimeter of the island and from the edge of the inner brackish-water lagoon. Due to the island’s geographic location in a low productivity zone, a lack of variable habitats on and surrounding the island, and heavy surf that pounds the exposed land, a depauperate fauna was recovered although mixed biogeographic affinities are represented. The shallow-water foraminiferal assemblage has no endemics but primarily tropical Indo-Pacific and eastern Pacific (Panamic) affinities, as well as one species of Caribbean affinity. The most abundant species are Sorites spp. and Quinqueloculina spp. Noticeably absent are any species of Amphistegina, despite the fact that they are considered ubiquitous in the tropical Pacific. The molluscan fauna has Clipperton Island endemics, a tropical Pacific/Inter-Island endemic, and tropical eastern Pacific oceanic islands/Panamic Molluscan affinities. The ostracods included endemics found restricted to Clipperton Island lagoon, as well as Indo-Pacific and Panamic Province species. The foraminifera, mollusks, and ostracods are thought to disperse to Clipperton Island by way of the North Equatorial Countercurrent and North Equatorial Current, suggesting that the island is indeed a stepping-stone for migration both east and west across the Eastern Pacific Barrier.