The first genetic linkage map of blackcurrant, published by Brennan et al. (2008), identified regions where QTLs for some important traits were located. The analysis was complicated by the fact that the mapping population was found to contain two subgroups, with segregation ratios consistent with these being crossed and selfed offspring. The crossed and selfed offspring were used for QTL analysis separately, and the QTL analysis was based on the trait mean over three years. Here we re-analyse two important traits, anthocyanin concentration and budbreak, using a mixed model multi-environment approach. The three years are considered as three separate environments, the data from both the selfed and crossed offspring are combined and different residual terms are explored to model the correlation between the years. This permits tests for interactions between the QTLs, the year and the type of offspring (selfed or crossed). Several additional QTLs were identified, some affecting the trait in both the selfed and crossed offspring, others in just one.