Over the past few decades, amphibian populations have undergone drastic declines on a global scale. Declines in many anuran populations have been linked to the emergent skin-invasive amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). Antimicrobial peptides in the skin are thought to act as important components of the innate immune system that may protect some species from infectious diseases. The four archaic species of Leiopelma in New Zealand are of great conservation concern and a severe population crash of Leiopelma archeyi between 1996 and 2001 has been tentatively linked with the outbreak of Bd. Here, we investigated the in vitro activity of skin secretions of six frog species in New Zealand against Bd zoospore growth. The activity of skin secretions produced by frogs in the wild varied significantly between species, with those of Le. archeyi being the most active. The skin secretions of native Leiopelmatid species showed greater Bd zoospore inhibition (31.0–71.9%) than the naturalized Litoria species (17.4–18.2%). Leiopelma archeyi has the most active peptides, even though it is the only native species with known susceptibility to Bd infections.