Nine-spined stickleback (Pungitius pungitius) is a good model species for studying personality traits such as boldness and aggression as large variation in these behaviours has been observed in populations from different habitats. Here we used genomic information from three-spined sticklebacks to identify and characterise 13 new nine-spined stickleback microsatellite loci which are located close to candidate genes for behaviour. All loci were polymorphic with 3–31 alleles per locus and expected heterozygosity varied from 0 to 0.97 and observed heterozygosity from 0 to 1. These markers should provide a useful resource for better understanding the genetic basis of behaviour in stickleback fishes.