In this dataset, we present white muscle and blood tissue samples of bigeye (Thunnus obesus) and yellowfin tuna (Thunnus albacares) collected by trained observers onboard commercial fishing boats (purse seine and longline) between 2001 and 2016 in the Southwestern Pacific, and a few other data for two other tuna species (Thunnus alalunga - albacore and Katsuwonus pelamis - skipjack). The dataset includes information from 170 sampled individuals, with muscle and blood tissue samples of each individual. Samples data include the individual’s ID, species ID (BET bigeye, YFT yellowfin, ALB albacore, SKJ skipjack), species name, sampling date, fork length (cm), geographical location (i.e., longitude and latitude, and Longhurst province modified according to Houssard et al. 2017), δ15N isotope value (‰), total mercury concentration (THg in µg.g‑1, dry weight) and tissue (blood or muscle).