Determining the factors that give rise to reproductive isolation is critical for understanding how species form. Observing reproductive isolation between closely related populations is especially interesting because it can show the factors initially involved in species formation. We studied two phenotypically different populations of Side-Blotched Lizards (Uta stansburiana), which diverged less than 22,500 years ago according to geologic evidence. The lava flow population has dark dorsal coloration for crypsis and is dimorphic for throat coloration used for signaling male mating type. The off-lava population has light dorsal coloration and is trimorphic for throat coloration. We tested whether there was reproductive isolation between these two populations in order to understand the factors that maintain the phenotypic differences between these populations. Our genetic crosses revealed evidence of reproductive incompatibilities because females from the dimorphic lava population produced fewer fertilized eggs and more unfertilized eggs when mated outside their population. In addition, male morphs varied in their reproductive compatibility because females from both populations produced fewer fertilized eggs and fewer clutches with orange-throated males from outside their population. The reproductive incompatibilities observed between the populations suggest that cryptic female choice of sperm may act as a post-mating, prezygotic barrier that contributes to the rapid formation of new species.