[1] Aphrosaurus was found below a different juvenile species, Morenosaurus stocki,[3] within the Tierra Loma Member of the Panoche Hills.

LACM 2832, found in the same formation, was also initially determined to be Aphrosaurus with ontogenic features, but that classification was rejected in a reappraisal on the basis of systemic differences between the two specimens that likely could not be explained by ontogeny.

[3] Welles took the name Aphrosaurus from the Greek for "sea foam" + "lizard", and furlongi in honor of University of California Berkeley field assistant and specimen preparator Eustace Furlong.

[7] A 2008 study by Zammit et al. using a model of the complete vertebral column and neck indicated that while Aphrosaurus and similar plesiosaurs would not have been able to create a "swan curve" of the neck to strike, other feeding methods, including benthic grazing, shallow horizontal curving for ambush, and horizontal or vertical shearing during active pursuit would have been possible.

The lack of plioplatocarpines was hypothesized by Lindgren and Schulp in 2010 to indicate an environment as an open ocean with high piscivore competition for resources.

Similar genera of mosasaurs in both the Moreno Formation and Western Interior Seaway indicates free exchange of species between both environments.

[12] Within the mostly morphologically similar elasmosaurids, Aphrosaurus can be differentiated by the presence of a deepened ventral notch along the centra of the cervical vertebrae, and a wide, dorsal-ventrally compressed interclavicle-clavicle complex that lacks a ridge along the sternum.

However, current phylogenetic studies have recovered Aphrosaurus in a highly nested position within the Weddellonectia clade, but outside of the Aristonectinae with the filter-feeding Aristonectes.