We introduce a new method that uses generalized linear mixed models to infer the depth distribution of pelagic fishes. It uses existing data from research surveys and observers on commercial vessels to estimate changes in catchability when longline fishing gear is lengthened to access deeper water. We infer the depth distribution of catchability for 37 fish species that are caught on pelagic longlines in the Pacific Ocean. We show how the estimates of catchability can be used to correct abundance indices for variations in longline depth. Our method facilitates the inclusion of data from early surveys in the time series of commercial catch rates used to estimate abundance. It also resolves inconsistencies in the time series caused by a rapid switch to deep longlining in the 1970s. The catchability distribution does not always match depth preferences derived from tracking studies. Therefore, depth preferences from tracking studies should not be used to correct abundance indices without additional information on feeding behavior.