A large number of autochthonous breeds of domestic animals are endangered. The Portuguese indigenous pig breed Bísaro is reduced to a small number of animals mostly restricted to the Trás-os-Montes province. In order to prevent its extinction and preserve genetic variability fast measures are needed. Among molecular markers to assess the genetic variability microsatellites are the most widely used. No such markers have yet been described to be specific for this breed. This work aims to identify VNTRs (Variable Number of Tandem Repeats) among the populations of Bísaro and to sequence their conserved flanking regions to develop primers for PCR (Polymerase Chain Reaction) amplification of microsatellites in order to assess the genetic variability within and among populations. Such data can be used in future selection programs. A large number of recombinant clones is being screened by hybridization using (TG)10 and (TC)10 synthetic oligonucleotides as probes and (TG)n microsatellites were found to be more frequent in this breed.