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This study provides 53 new fluorescent in situ hybridization cytogenetic assignments for microsatellite markers linked to the swine genetic map. Forty microsatellites are physically assigned for the first time. The chromosomal locations of eight markers were either confirmed or refined, while five loci were assigned to locations different from those given in previous reports. Markers were selected to provide physical anchors based on their presumed proximity to centromeres or telomeres and at approximately 30 cM invervals across the genetic map. The number of physical anchors for pig (SSC) chromosomes 8, 15, and 18 linkage groups was significantly improved. Centromeric regions were localized to areas less than 10 cM for SSC 1, 2, 3, 6, 7, 8, and 9. Although the recombination rate was generally higher across small biarmed chromosomes and lowest for large arocentric chromosomes, two regions with particularly low (1q2.1→q2.9 and 13q2.3→q4.1) and three regions with extremely high (5p1.5→p1.2, 6p1.4→p1.3, and 12p1.5→p1.4) rates of recombination were detected. These assignments represent an overall 10% increase in the number of physically assigned markers in Sus scrofa and more than a 20% increase in the number of Type II loci assigned to the pig cytogenetic map.