Introduced juvenile Chinook salmon (Oncorhynchus tshawytscha) have been found co-occurring with native fishes in the Allipén River, Chile. Due to this co-occurence, the microhabitat use, microhabitat preferences, and overlap between juvenile Chinook salmon and the native catfish, Trichomycterus areolatus, were examined during the summer and fall of 2007-2008. Microhabitat preferences and overlap between juvenile Chinook salmon and the native catfish were determined using the Instream Flow Incremental Methodology and the Pianka´s index. Juvenile Chinook salmon and the native catfish microhabitat preferences varied seasonally showing a high degree of similarity and overlap between the species (higher than 80%). The results suggest the risk of negative interactions and interactive segregation over habitat processes between juvenile Chinook salmon and native catfish. As a consequence, the Chinook salmon invasion may threaten the stability of native catfish populations at Allipén River.