Ontogenetic conflict arises when optima for alleles governing fitness variation differ between juveniles and adults or between adult sexes. Loci that govern development of alternative phenotypes in the sexes, hereafter termed morph-determining loci, mediate development through the endocrine system. Morphotypic selection is defined to be multivariate selection favoring discrete alternative morphotypes (e.g., optima). When the optimal combinations of alleles for alternative morphs differ between the sexes, it generates conflicting selection pressure and thus ontogenetic conflict. Selection on morph alleles promotes ontogenetic conflict because it perturbs physiological epistasis that governs the expression of male versus female traits. Expression of physiological traits arises from homeostasis that maintains trait expression within a normal range. The genetic basis of homeostasis is likely to arise from interactions among several genes (e.g., genetic epistasis) or protein products (e.g., physiological epistasis). For example, endocrine regulation arises from interactions between gondatropins, which are protein hormones produced by the hypothalamic-pituitary glands, and steroid hormones, which are produced by the gonads (e.g., HPG axis). The side-blotched lizard system is discussed with respect to physiological bases of ontogenetic conflict. We also describe a novel molecular marker strategy for uncovering genome-wide physiological epistasis in nature. Finally, ontogenetic conflict exerts selection on females to evolve mate selection or cryptic choice that is reflected in different sires being chosen for son versus daughter production. We describe how side-blotched lizard females ameliorate ontogenetic conflict by cryptic choice of male genotypes to produce sons versus daughters.