In most vertebrates, teeth are continuously shed and replaced throughout life, while mammals and several lineages of reptiles have reduced replacement to only one or two generations. In contrast to the vast majority of their living relatives, members of the lizard families Chamaeleonidae and Agamidae have dispensed with lifelong tooth replacement, instead developing acrodont dentition that fuses to the jawbone to be used for the lifetime of the animal. Though, the loss of tooth replacement has not come without a cost. In order to mitigate the consequences that come with tooth replacement loss, mammals and acrodont lizards have evolved adaptations that strengthen enamel structure and minimize wear and tear experienced during the life of the animal. While these physical adaptations are well documented, the effect that loss of tooth replacement has had on the molecular components of teeth has not received significant attention. Here, we analyze the coding and amino acid sequences of six tooth proteins (AMBN, AMEL, AMTN, ACP4, ENAM, and MMP20) from acrodont lizards, pleurodont lizards that replace teeth, and mammals. We show that the reduction of tooth generations has disproportionately affected the evolutionary trajectory of proteins associated with enamel structure, with a particularly magnified effect on the evolution of AMEL.