Goat is believed to be the first true livestock domesticated and, apart from its historical importance, keeps playing an essential economic role in very diverse human societies. We have analysed the female gene pool of all Portuguese autochthonous breeds (Bravia, Serrana, Charnequeira, Serpentina and Algarvia) through the mtDNA HVI sequencing of 288 unrelated animals sampled throughout the country. All breeds proved to be extremely diverse (average haplotype diversity of 0.977), in contrast with the Portuguese peripheral geographic situation in the distribution range of the species. Moreover, observed genetic distances between breeds do not correlate with microgeography inside Portugal. These observations are consistent with recurrent refreshment of the breeding stock through the introduction of exotic animals. Fitting the new data into the still loosely defined female genetic pool landscape of goats, all Portuguese animals, one sample excepted (belonging to Bravia), are classified into haplogroup A and haplotype sharing is geographically very sparse, including a Far East match. Our results confirm that goats stand out among most of domesticates as exceptionally diverse and showing an unparalleled degree of mobility of animals (at least females) used for reproductive purposes.