Due to the tight linkage among the casein genes, the study of the haplotype variability is a necessary approach in order to identify important effects which could be exploited for the genetic improvement of goat species, showing considerable casein genetic variation. The aim of this paper was to analyse the casein haplotype distribution, with particular attention to the linkage phase between as1-casein (CSN1S1) and b-casein (CSN2). The two first loci of the casein cluster, which are only 12 kb apart and are convergently transcribed. Apulian goats from Garganica, Jonica, and Maltese breeds were considered. DNA typing showed that the CSN2*C allele is mainly associated to CSN1S1*A and CSN1S1*F allele. Most probably, the differentiation between CSN2*C and CSN2*A occurred before the numerous mutations affecting CSN1S1 locus
