An analysis of protein variation at three loci (transferrin, guanine deaminase, and an esterase) in sets of blood samples taken from single schools over four years off the coast of New Zealand is reported. There were no significant variations in allele frequency between sample sets for transferrin. The esterase data were heterogeneous, showing significant within‐ and between‐year variations in allele frequency. Esterase allele frequencies changed with the average size of fish in the school. There was no difference between the estimated esterase allele frequencies of eastern and western coast schools. In most cases the esterase and guanine deaminase allele frequencies observed were similar to those found for schools in tropical waters to the north of New Zealand. However, some schools had frequencies similar to those of schools from French Polynesia and others similar to those from schools from Papua New Guinea and the Solomon Islands. The results obtained are considered in the light of various discrete stock models and an isolation‐by‐distance model of the Pacific skipjack tuna population.