Multilocus microsatellite genotype (11-13 loci) of all mother-calf pairs and candidate males used in the paternity analysis in the publication. The data are in a format suitable for analysis in the program CERVUS (Kalinowski et al 2007). Source of samples: Surveys were conducted from small vessels (4.6-5.2 m) at Port Ross, Auckland Islands (50° 32’S, 166° 15’E) during the austral winters of 1995-1998 and 2006-2009 as described by Patenaude et al. (2001) and Carroll et al. (2011b). Around the North and South Islands of NZ (mainland NZ), biopsy samples were collected opportunistically by NZ Department of Conservation employees using a modified veterinary capture rifle (Krützen et al. 2002). Skin samples were preserved in 70% ethanol on location and transferred to the University of Auckland for storage at -20°C. Sample analysis:Total genomic DNA was extracted from skin biopsy samples using standard proteinase K digestion and phenol/chloroform methods (Sambrook et al. 1989), as modified for small samples by Baker et al. (1994). Molecular identification of sex and sequencing of the mtDNA control region (500 bp) was conducted following methods previously described in detail by Carroll et al. (2011a). Samples were genotyped using 13 microsatellite loci (GT23; Bérubé et al. 2000; TR3G1, TR3G2, and TR3F4; Frasier et al. 2006; GATA28 and GATA98; Palsbřll et al. 1997; EV1, EV37 and EV14; Valsecchi & Amos 1996; RW18, RW31, RW410, and RW48; Waldick et al. 1999) as described in Carroll et al. (2011b). Only samples that amplified at a minimum of 11 or more loci were included in further analyses to improve the power of the paternity assignment. Further details on sample collection, laboratory methods, quality control procedures and estimated error rates can be found in Carroll et al (2011a,b) and in the publication associated with the dryad archive. For more information see: Patenaude NJ, Baker CS, Gales N (1998) Observations of southern right whales on New Zealand's subantarctic wintering grounds. Marine Mammal Science 14, 350-355. Patenaude NJ, Baker CS (2001) Population status and habitat use of southern right whales in the sub-Antarctic Auckland Islands of New Zealand. Journal of Cetacean Research and Management Special Issue 2, 111-116. Carroll EL, Patenaude NJ, Alexander AM, et al. (2011a) Population structure and individual movement of southern right whales around New Zealand and Australia. Marine Ecology Progress Series 432, 257-268. Carroll EL, Patenaude NJ, Childerhouse S, et al. (2011b) Abundance of the New Zealand subantarctic southern right whale population estimated from photo-identification and genotype mark-recapture. Marine Biology 158, 2565-2575.