Onboard observer programs are key to collect data for fishery dynamics analysis and species bycatch and discard estimation. Major sources of bias of onboard sampling for catch data collection concern the vessel selection method, representativeness of catch sampling data and changes in fishing behavior in the presence of observers. This study was motivated by the worldwide issue of low number of vessels included in the sampling frame due to several types of refusals, and the representativeness of the samples for obtaining accurate catch estimates. Analyses were performed using trips from a bottom otter trawl (target fleet) and from the sampling frame, with and without observers onboard. Multivariate analysis of trips was conducted using logbook data, including landings, trip duration, fishing hours and spatial information, but not discards. Two groups of fishing trips were identified within the target fleet during the study period (2012−2015) with distinct fishing regimes, total landings and main landed species. Vessels from the sampling frame were representative of the target fleet and no observer effects occurred in the sampled trips. These findings support the assertion that the sampling frame used is an indicator fleet and analogous to a reference fleet. Cluster-based discard approaches improved the discard estimates precision, when compared to the fleet-based, in particular the cluster stratified approach. Our study suggests that the implementation of a threshold on the species prevalence in discards may potentially introduce bias in the estimates. Discard estimation without applying a threshold, with fleet- or cluster-based approach, should be ultimately dictated by end-users need, based on the trade-off between bias and variance.