Species conservation depends on robust population assessment. Data on population abundance, distribution, and connectivity are critical for effective management, especially as baseline information for newly documented populations. I describe a pygmy blue whale (Balaenoptera musculus brevicauda) population in New Zealand waters with year-round presence that overlaps with industrial activities. This population was investigated through a multidisciplinary approach, including analysis of survey data, sighting records, acoustic data, identification photographs, and genetic samples. Blue whales were reported during every month of the year in the New Zealand Exclusive Economic Zone, with reports concentrated in the South Taranaki Bight (STB) region, where foraging behavior was frequently observed. Five hydrophones in the STB recorded the New Zealand blue whale call type on 99.7% of recording days (January-December 2016). A total of 151 individuals were photo-identified between 2004 and 2017. Nine individuals were resighted across multiple years. No matches were made to individuals identified in Australian or Antarctic waters. Mitochondrial DNA haplotype frequencies differed significantly between New Zealand (n = 53 individuals) and all other Southern Hemisphere blue whale populations, and haplotype diversity was significantly lower than all other populations. These results suggest a high degree of isolation of this New Zealand population. Using a closed capture-recapture population model, our conservative abundance estimate of blue whales in New Zealand is 718 (95% CI = 279-1926). These results fill critical knowledge gaps to improve management of blue whale populations in New Zealand and surrounding regions. Limited knowledge of population structure has hindered management of blue whales in the Southern Hemisphere in the past. I have shown how a multidisciplinary research approach, applied to one particular region in this case, can enhance our global understanding of population structure.