Few descriptions of the development and sequence of chondrification and ossification of the entire skeleton of turtles exist, particularly compared to other groups of reptiles. In this study, the embryonic skeleton and its ontogenesis are described for the Alligator Snapping Turtle, Macrochelys temminckii (Chelydridae). Morphological descriptions utilize cleared and double-stained embryonic specimens and form the basis of comparison of the ontogenesis of the skeleton between this species and its extant sister taxon, Chelydra serpentina. The embryonic chondrocranium, as well as the sequences of formation and ossification of the entire skeleton, are compared between these closely related species, and afford a unique opportunity to examine differences in their patterns of skeletal formation. In M. temminckii, the first elements to ossify (Stage 17) are associated with the dermatocranium and upper jaw, followed by elements of the palate, lower jaw, and long bones of the limbs. In both species the majority of endochondral braincase elements (prootic, opisthotic, supraoccipital, and exoccipital) ossify after the majority of dermal elements of the skull. The sequences of formation of the chondral primordia of the limb elements, as well as ossification of autopodial elements, are generally congruent between these species. J. Morphol. 263:71–106, 2005. © 2004 Wiley-Liss, Inc.