The worldwide decline in frogs has been linked to a deadly disease (Chytridiomycosis) caused by the chytrid fungus, Batrachochytrium dendrobatidis. We used Congo red to study chytrid fungi in skin scrapings taken from formalin preserved animals, from non-preserved decaying or dead animals, as well as from apparently healthy animals. We were able to distinguish immature and mature zoosporangia, zoospores and germling stages of the fungus within the host tissue. Staining patterns varied. Zoospores (including flagellum) stained orange but the walls of all other stages stained a reddish-orange. The inoperculate discharge tube was always intensely stained. However, when zoosporangia were within intact epidermal cells, only the exposed discharge tube stained unless the keratinized layer was breached. The epidermal cells either did not stain or stained pale orange. Congo red is cheap, easy to use and relatively non-hazardous, making it a valuable tool to study the spread and role of chytridiomycosis in frog decline.