For desert fishes in the American Southwest, predation by invasive species has triggered massive population declines for decades, leaving researchers speculating on the underlying cause. It has been shown that Post-Pleistocene isolation of desert fishes in small habitats with limited predation pressure has led to loss of antipredator traits. Determining the status of antipredator behavioral and morphological traits could identify the most vulnerable desert fishes. In aquatic ecosystems, detection and response to chemical alarm cues derived from epithelial tissue increases the probability of predation survival. In chapter two, I evaluate alarm cue responses of two desert cyprinodontids: endangered Pahrump poolfish and Amargosa pupfish. In chapter three, I assess the prevalence and densities of epithelial club cells, the source of chemical alarm cues, for several desert fishes: Pahrump poolfish, Amargosa pupfish, White Sands pupfish, White River Springfish, and Hot Creek Valley tui chub.