Chilean Patagonia (41∘00’–57∘00’S) is among the least researched ocean regions in the world but supports commercial fisheries for several fish species, including the pink cusk-eel (Genypterus blacodes). Fishery monitoring of this species in fjords is fragmented, thus limiting the quality and quantity of useful information for stock assessment purposes. We proposed a methodological approach to constructing an abundance index for pink cusk-eel, based on catch per unit of effort surveys in the fjords and inner channels of Patagonia in three administrative regions in Chile (Los Lagos, Aysén, and Magallanes). Information regarding the definition of areas to be sampled and the related operational characteristics were gathered by interviewing fishers. Two research surveys were conducted on board artisanal longline vessels in each administrative region during autumn and spring of 2018. Within each region, 12 fishing grounds were sampled using a standardised protocol for soaking times, number of hooks per line and type of bait, and information was also recorded on target and bycatch species. In the Los Lagos region, the mean catch rate of pink cusk-eel was 3.5 and 4.1 fish/100 hooks on the first and second surveys, respectively. For the Aysén region, the mean catch rate of pink cusk-eel was 1.9 fish/100 hooks in the first survey and 6.6 fish/100 hooks in the second survey. The catch rates of pink cusk-eel on the Magallanes region were low, with only 0.5 fish/100 hooks in the first survey and 0.7 fish/100 hooks in the second survey The main teleost species in the bycatch were tadpole codling (Salilota australis) and rockfish (Helicolenus lengerichi), while the elasmobranch species were dogfish (Schroederichthys chilensis) and yellownose skate (Zearaja chilensis). The mean lengths of pink cusk-eel and tadpole codling showed a latitudinal gradient. This manuscript proposes recommendations and gives insights regarding the design and implementation of surveys over extensive and remote areas with unfavourable weather conditions and where fishery monitoring is fragmented.