The diel vertical migration of fish and larvae of the phantom midge Chaoborus flavicans was studied using a combined 38 and 200 kHz echo sounder. Multi-mesh gill net was used to sample fish, and a Schindler-Patalas trap to sample Chaoborus. Oxygen and temperature profiles were also recorded. At 38 kHz, only fish were detected, without considerable interference from Chaoborus echoes. At 200 kHz, both fish and Chaoborus were detected and echoes from Chaoborus almost completely masked all fish echoes at night. During the day, Chaoborus remained hidden in an oxygen-poor refuge near the bottom. Tracks of fish diving into the Chaoborus refuge were observed on several occasions. At the onset of dusk, Chaoborus started to rise and by the time it was dark they were occupying the whole water column. Fish were found in patches in midwater during the day. In the dark, the fish were dispersed throughout the water column. Results suggest that a dual-frequency approach can be used to discriminate between fish and Chaoborus and to provide a rapid method for their selective monitoring.