During an intensive meiofauna sampling campaign in intertidal seagrass beds along the Caribbean coast of the Yucatán Peninsula (Mexico), 131 specimens of Lightiella incisa (Cephalocarida, Crustacea) were recovered from the sediment. Two-thirds of the specimens were adults, one-third were pre-adults. This collection is the first record of this minute primitive crustacean in the western part of the Caribbean Sea, and extends the known range 3000 km from the type locality of Hastings Bay, Barbados. A detailed sampling protocol and environmental data made it possible to study the microhabitat preferences of this species, and perhaps for cephalocarids in general for the first time. The vertical distribution of L. incisa in the sediment showed a maximum density in deeper layers, i.e. 3–4 and 4–5 cm depth. Nitrate and nitrite concentrations seem to be most closely related to the distribution of L. incisa. It was clear that L. incisa followed polychaetes to deeper sediment layers. In this study we state that L. incisa is an endobenthic species occupying anoxic sediments oxygenated by bioturbation (e.g. Polychaeta) rather than being an animal living in the oxygenated top layers.