Surficial sediments rich in apatite pellets were recovered from an 80‐m‐deep area that runs parallel to the eastern coast of Vizcaino Bay, Baja California. This area is subject to intense seasonal upwelling, the sediments presenting elevated phosphate (P2O5), organic carbon (Corg), and carbonate concentrations. The pellets are moderately well sorted, concentrated mainly in the 3ø size class within a poorly sorted sediment matrix. Abundant nodular apatite and phosphatized bone fragments were found in only one of the pellet‐bearing samples. This sample has a P2O5concentration of over 20%, the ≥ — 2.5ø to 0.5ø grain size classes alone being formed of up to 32% P2O5. The high proportion of fragmented nodules and the presence of volcanic rock pebbles indicate that at least part of this deposit is allochthonous. The apatite pellets have a flat to concave‐downward heavy rare earth (HREE) shale normalized pattern and, except for La, are depleted in light rare earth elements (LREE). The close resemblance between the HREE patterns and the relatively high La concentration in the pellets of Vizcaino Bay, and the onland phosphorites of the southern Baja California Peninsula, suggest similar depositional histories for these deposits. No significant Ce anomalies were observed, but a negative Eu deviation is common in all of the pellet‐bearing sediments. The depletion of LREE in the pellets of Vizcaino Bay may indicate the preferential removal of these elements by weathering processes.