Cranial and postcranial elements attributed to the alligatoroid Bottosaurus harlaniMeyer, 1832, are described from the Rowan Fossil Quarry, a Cretaceous–Paleogene locality in Mantua Township, New Jersey, U.S.A. This specimen (NJSM 11265) represents the most complete individual attributable to the species and includes significant postcranial elements not found in other specimens. Posterior elements of the skull are described for the first time, and the species is placed into a phylogenetic context. Aspects of the skull table, including constricted supratemporal fenestrae, a linear frontoparietal suture, and a large trapezoidal dorsal supraoccipital exposure, are similar to those of caimans. Bottosaurus harlani is included within Caimaninae due to its possession of a linear frontoparietal suture between the supratemporal fenestrae. Optimal trees from phylogenetic analysis recover B. harlani in three different positions, as a sister either to the modern dwarf caimans (Paleosuchus), to living species of Paleosuchus, or to both. That a substantial stratigraphic gap separates B. harlani from both species of Paleosuchus, which first appears in the Miocene, along with low character and nodal support, raises questions about this relationship. The phylogenetic placement of B. harlani may reflect incomplete knowledge of the taxon, and further study might support placement outside of Caimaninae. More complete analyses of B. harlani and other Cretaceous–Paleogene alligatoroids will help to illuminate the relationships among these forms and their living relatives.