This study aimed at identifying gene markers associated with wool quality traits in Merino and Merino Cross sheep using a candidate gene approach. Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis was used to identify sequence variation in the KAP1.3 and K33 genes, while agarose gel electrophoresis was used to detect length variation in the KAP1.1 gene. Two half-sib families (SL1 and SL2) were created for analysis and wool samples were collected from the mid-side region of the SL1 progeny at 12, 24 and 36 months of age, and of the SL2 progeny at 12 months of age. The association of alleles was analysed for each year of phenotypic data by an analysis of variance (ANOVA) tests, using SPSS® version 15. Analysis of each of KAP1.1, KAP1.3 and K33 genes revealed potential gene markers to select for animals with increased staple length, increased staple strength, higher yield, whiter and brighter wool. The results obtained are consistent with KAP1.1, KAP1.3 and KRT1.2 being clustered on one chromosome. Results also indicated that the keratin genes on chromosome 11 are recombining relatively frequently at recombination “hotspots”. It appears as though genes coding for the KRTs and KAPs have the potential to impact on wool quality and could potentially be exploited in gene marker-assisted selection programmes in the wool industry for the rapid conversion of wool from one type to another.