One of the most urgent problems in conservation biology today is the continuing loss of amphibian populations on a global scale. Recent amphibian population declines in Australia, Central America, the western United States, Europe, and Africa have been linked to a pathogenic chytrid fungus, Batrachochytrium dendrobatidis, which infects the skin. The skin of amphibians is critical for fluid balance, respiration, and transport of essential ions; and the immune defense of the skin must be integrated with these physiological responses. One of the natural defenses of the skin is production of antimicrobial peptides in granular glands. Discharge of the granular glands is initiated by stimulation of sympathetic nerves. To determine whether antimicrobial skin peptides play a role in protection from invasive pathogens, purified antimicrobial peptides and natural peptide mixtures recovered from the skin secretions of a number of species have been assayed for growth inhibition of the chytrid fungus. The general findings are that most species tested have one or more antimicrobial peptides with potent activity against the chytrid fungus, and natural mixtures of peptides are also effective inhibitors of chytrid growth. This supports the hypothesis that antimicrobial peptides produced in the skin are an important defense against skin pathogens and may affect survival of populations. We also report on initial studies of peptide depletion using norepinephrine and the kinetics of peptide recovery following induction. Approximately 80 nmoles/g of norepinephrine is required to deplete peptides, and peptide stores are not fully recovered at three weeks following this treatment. Because many species have defensive peptides and yet suffer chytrid-associated population declines, it is likely that other factors (temperature, conditions of hydration, “stress,” or pesticides) may alter normal defenses and allow for uncontrolled infection.