Despite their economical importance, relatively few molecular studies have been made on goats compared to other livestock species. The most recent goat map was published in 1998, and lacks complete genome coverage. A large number of discrepancies and especially inter-chromosomal re-assignments were reported between the 1998 goat linkage map and the sheep map. In this study 94 microsatellite markers were amplified in 12 half-sib South African Angora goat families for compilation of a genetic map, aiming to confirm or reject previously reported rearrangements and to improve the alignment between the ovine and
caprine maps. The number of informative meiosis per marker ranged from 69 to 836, with an average of 518. The microsatellites were mapped to 23 chromosomes, spanning 1352 cM and resulting in an average marker interval of 23.0cM. Marker orders were compared to the previously published goat maps, as well as to the ovine map. Six chromosomes(CHI2, 4, 5,11,13 and 19) showed rearrangements in marker order compared to the 1998 Schibler
et al. goat map, while nine previously unmapped markers were conclusively assigned to eight chromosomes. Four of the previously reported in tra-chromosomal rearrangements between the goat and sheep maps were confirmed to be either population specific or mapping errors. The verification of rearrangements in loci order will lead to improved alignment between the two maps, as well as improved efficiency of genome and fine mapping efforts in goats.