The Puelo and Petrohué rivers were surveyed between April 2016 and February 2017 to assess the presence and seasonal abundance of Didymosphenia geminata in the wild aquatic systems of these two important rivers in southern Chile. Didymo was reported in the Puelo River in 2012, while it was declared absent from the Petrohué River before this study commenced in the fall of 2016. Results showed that cells of D. geminata were recorded in both rivers, in the Phytobenthos as well as in the water column. However, the classical mucilage which characterizes this plague was only recorded in one of the sampled rivers (Puelo). The mucilage was not recorded in any of the sections sampled in the Petrohué River, which was attributed to the high concentration of phosphorous present in the system. The concentration of phosphorous recorded throughout the study in the Puelo River was low. However, differences in the recorded presence or absence of D. geminata between sampling sites on the Petrohué River was mainly attributable to the availability of incident sunlight. This study records for the first time the presence of D. geminata in the Petrohué River.