Catch per unit of effort (CPUE) needs to be standardized to remove the effects of factors such as fishing time and location, before it can be used as an index of abundance in fish stock assessments. One of the most substantial effects arises from a change of target species. This is particularly important for the Taiwanese distant-water longline fishery, which has a long history of fishery data from two fleets that target various tuna species across three oceans. We review the development of the Taiwanese distant-water longline fishery and compare five designs for standardizing the catch rate of yellowfin tuna (Thunnus albacares) in the western and central Pacific Ocean, using generalized linear models with lognormal and delta-lognormal error assumptions. Two approaches to address targeting effects were tested: separating fishing fleet data based on observer records, and including four target indicators calculated from catch data. Four statistical regions (relating to major fishing grounds) were treated as a single factor in the first three cases and were treated separately for the last two (one independent run for each region). The last case, which involved independent analyses for each fishing fleet for each region, and using the delta-lognormal approach, was considered to provide the most informative standardized CPUE trends for yellowfin tuna.