Allele frequency data for 13 microsatellite loci for the southwest Australian southern right whale subpopulation. The data are in a .ALF format suitable for analysis in the program CERVUS (Kalinowski et al 2007). Source of samples: samples were collected from Western and South Australia. The original references for the samples are Baker et al (1999) and Carroll et al (2011). 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; Palsbĝll 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: Baker CS, Patenaude NJ, Bannister JL, Robins J, Kato H (1999) Distribution and diversity of mtDNA lineages among southern right whales (Eubalaena australis) from Australia and New Zealand. Marine Biology 134, 1-7 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.