Phosphorylation of caseins (CN) is a crucial post-translational modification that allows caseins to form colloid particles known as casein micelles. Both alpha(S1)-and alpha(S2)-CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than beta- and kappa-CN. However, little is known about the genetic background of individual alpha(S2)-CN phosphorylation isoforms and the phosphorylation degrees of alpha(S1)- and alpha(S2)-CN (alpha(S1)-CN PD and alpha(S2)-CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total alpha(S1)- and alpha(S2)-CN, respectively. We aimed to identify genomic regions associated with these traits using 50K single nucleotide polymorphisms for 1,857 Dutch Holstein Friesian cows. A total of 10 quantitative trait loci (QTL) regions were identified for all studied traits on 10 Bos taurus autosomes (BTA1, 2, 6, 9, 11, 14, 15, 18, 24, and 28). Regions associated with multiple traits were found on BTA1, 6, 11, and 14. We showed 2 QTL regions on BTA1, one affecting alpha(S2)-CN production and the other harboring the SLC37A I gene, which encodes a phosphorus antiporter and affects alpha(S1)-and alpha(S2)-CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual alpha(S1)-CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for beta-lactoglobulin and affects relative concentrations of alpha(S2)-CN-10P and alpha(S2)-CN-11P as well as alpha(S1)-CN PD and alpha(S1)-CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of alpha(S1)-CN-10P and alpha(S2)-CN-11P as well as alpha(S1)-CN PD and alpha(S2)-CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of alpha(S1)-CN and alpha(S2)-CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in alpha(S1)- and alpha(S2)- phosphorylation in Dutch Holstein Friesian require further investigation.