The red cusk-eel (Genypterus chilensis, Guichenot, 1848) is an iconic species in Chilean gastronomy, with a cultural significance that extends beyond its economic value, worthy of conservation. Despite the decline in fishery productivity across most of the distribution range for this species, little effort has been devoted to assessing stock management. In the present study, seven heterologous microsatellite loci (cmrGb3.8.1, cmrGb5.2B, cmrGb4.2A, cmrGb4.2B, cmrGb5.9, cmrGb4.11, and cmrGb2.6.1)

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... were genotyped in a total of 153 individuals from four locations in central and southern Chile (30.5-37.6 • S), comprising ∼1,000 km of coastline. Five microsatellite loci were consistently amplified with a low frequency of null alleles (<2.5%). These markers showed high average heterozygosity (H O = 0.886 and H E = 0.884) and PIC (0.869). Significant genetic differentiation among locations (global F ST = 0.043, global D Jost = 0.252) suggested the presence of at least two genetic groups along the Chilean coast, with moderate levels of admixture between the two central populations (0.168 < Q mean < 0.822). The southern population showed no admixture with the central populations (Q mean = 0.985), less allelic richness and a small effective population size, indicating that urgent management measures must be developed for this fishery. The present study provides baseline information to assist fishery and aquaculture management and contribute to the recovery of declining populations.