Purification of α-1,4-glucan lyase from red algae and fungi has previously been reported. The α-glucan lyase converts α-glucans to 1,5-anhydro-D-fructose. In this study, an endophyte was detected between the algal cells of Gracilariopsis sp., but not penetrating the cell walls. Histological staining was consistent with the endophyte being fungal and immunohistochemistry revealed that it possessed an α-1,4-glucan lyase differing from that of the host. The endophyte α-glucan lyase was recognized by antisera against both fungal and red algal α-glucan lyases, whereas the α-glucan lyase found in the algal tissue was recognized only by the antisera against algal α-glucan lyase. The lyases occur independently in the host and in the endophyte, and were sometimes detected simultaneously. The endophyte was only observed in Gracilariopsis sp. collected in China; no endophyte could be detected in Gracilariopsis sp. from California or in Gracilaria chilensis.