AbstractMilk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome‐wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano‐Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome‐wide significant QTL for lactose percentage on chromosome 2 (129.77–131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8–94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation‐specific genetic determinants. In Analysis 2, we identified several genome‐wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano‐Granadina goats.