Several attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close-kin mark–recapture (CKMR) methods provide information about the number of adults in a population using close-kinship pairs identified by genetic markers and statistical methods. In this study, we compared three methods for kinship identification using different algorithms in samples of wild Pacific bluefin tuna genotyped across 5,029 genome-wide single nucleotide polymorphisms in 4,108 samples. The fraRF method we developed employs pairwise identity-by-descent values as inputs for random-forest classification. The other two methods were CKMRsim and COLONY, which have been applied in several studies. These three methods were applied to the actual genotyping data, in addition to the pseudo-generated genotyping data for the simulation test. The simulation test mimicked genotyping data with physical linkage as well as genetic characteristics similar to those of actual samples. The three methods resulted in different numbers of inferred kinship pairs for both generated and actual data. Particularly, the identification result of half-sibling pairs indicated the difficulty of identifying it. The difference in kinship identification results were interpreted based on a simulation test. This study may contribute to the selection and usage of statistical methods for different target species in future CKMR studies.