Journal of Fish Biology (1998) 52, 665–676 Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA T. D. B*‡  J. B. D † *Department of Fisheries and Oceans, Science Branch, Pacific Biological Station, Nanaimo, B.C., Canada V9R 5K6 and †Department of Fisheries and Oceans, Science Branch, P.O. Box 5667, St John’s, Newfoundland, Canada A1C 5X1 (Received 24 M ay 1997, Accepted 1 November 1997) Variation at four microsatellite loci was examined for three populations of Atlantic salmon Salmo salar from the Conne River, Newfoundland. Samples of wild parr were collected from the mainstem Conne River during 4 years, and from tributaries Twillick Brook and Bernard Brook during 2 years. No significant temporal variation was observed in allele frequencies at the Ssa14, Ssa197, Ssa202, and Ssa289 loci. No difference in allele frequencies was observed between parr from Bernard and Twillick brooks at any locus, but allele frequencies of mainstem Conne River parr were significantly different from those of the tributaries at Ssa14 and Ssa202, indicative of differentiation among local populations. Atlantic salmon from the Conne River system were well differentiated from those in Nova Scotia, Canada and from those in Europe.  1998 The Fisheries Society of the British Isles Key words: microsatellite; Salmo salar; genetic variability; local population differentiation. INTRODUCTION The genetic structure of populations spawning within rivers, as well as the ability to differentiate populations between rivers, is of interest for both Pacific and Atlantic salmon management. In Pacific salmon, protein electrophoresis has been used extensively in mixed-stock fisheries management (Beacham et al., 1987; Shaklee et al., 1990), but the limited variation detected at allozyme loci for Atlantic salmon Salmo salar L. (Stahl, 1987; Jordan et al., 1992) generally has restricted applications in management, although some are potentially available (Koljonen & McKinnell, 1996). DNA technology has provided the ability to detect greater differentiation among populations than found normally at allozyme loci. Substantial differentiation among populations has been observed at minisatellite DNA loci in both Pacific (Beacham et al., 1996; M iller et al., 1996) and Atlantic salmon (Taggart et al., 1995; Galvin et al., 1996). Variation at microsatellite DNA loci is also quite useful in determining the genetic structure of Pacific (Scribner et al., 1996) and Atlantic salmon populations (McConnell et al., 1995a, b; O’R eilly et al., 1996; Sanchez et al., 1996). DNA technology aids substantially in the determination of fine-scale population structure in salmonids as recently demonstrated, for example, by Angers et al. (1995), who used microsatellites with amplification by the polymerase chain reaction (PCR). ‡Author to whom correspondence should be addressed. Tel.: 250-756-7149; fax: 250-756-7053; email: beachamt@dfo-mpo.gc.ca 665 0022–1112/98/040665+ 12 $25.00/0/jb970610  1998 The Fisheries Society of the British Isles