Introduction Seals are potential competitors with commercial fisheries for the same basic resources: fish and cephalopods. Around the UK coast there is concern that both grey seals Halichoerus grypus and harbour seals Phoca vitulina may impact fisheries, and considerable research effort has been put into assessing their diet (Prime & Hammond 1990; Pierce et al. 1991a,b; Hammond et al. 1994; Tollit & Thompson 1996). Such studies have generally been based on analyses of prey hard parts (fish otoliths and cepha- lopod beaks) recovered from scat samples (Pierce & Boyle 1991). Hard part analysis is a noninvasive technique and allows dietary data to be gathered from many animals, but is constrained because scat samples cannot be assigned to seal species or individual seals. Species identification is necessary because grey and harbour seals form mixed species haul-out groups in many areas around the UK. Data from radio telemetry and satellite tracking studies of grey and harbour seals have shown that while harbour seals tend to forage in relative- ly restricted inshore areas with average foraging ranges of a few tens of kilometres, grey seals tend to range much more widely, moving between foraging sites that may be more than 100 km distant (Thompson et al. 1991; 1993, 1994; McConnell et al. 1992, 1994). These data suggest that the diets of the two species, although hauling out in the same areas, may differ considerably. Even where sites are used by only one species, there may be considerable intraspecific variation in diet. Sex- and age-related differences in body size may influence diet (Frost & Lowry 1986). Studies of other marine mam- mals also suggest that individual differences in foraging techniques (Hoelzel et al. 1989) and foraging areas (Clapham & Mayo 1987; Thompson & Miller 1990) could result in individual variation in diet within a population. To study feeding preferences amongst seals, serial sam- ples must be obtained from the same individual. In some Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces J. Z. REED, D. J. TOLLIT,* P. M. THOMPSON* andW. AMOS University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK, *University of Aberdeen, Department of Zoology, Lighthouse Field Station, Cromarty, Ross-shire IV11 8YJ, UK Abstract Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat sam- ples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition. Scat samples have been collected from intertidal haul-out sites around the inner Moray Firth, north-east Scotland. We have assessed methods to extract and purify faecal DNA, a combination of DNA from the individual seal, prey items, and gut bacteria, for use in PCR. Controls using faecal and blood samples from the same individual have enabled microsatellite primer sets from four pinniped species to be tested. Approximately 200 scat samples have been examined for species identity and individual matches. This study will provide essential information for the assessment of interactions between seals and com- mercial or recreational fisheries. Keywords: microsatellites, VNTR, DNA extraction, faecal DNA, diet, pinnipeds Received 10 June 1996; accepted 9 September 1996 Molecular Ecology 1997, 6, 225–234 Correspondence: Jane Z. Reed. University of Cambridge, Department of Zoology, Cambridge CB2 3EJ. Tel.: +44-(0)1223- 336677. Fax: +44-(0)1223-336676. E-mail: jzr@mole.bio.cam.ac.uk © 1997 Blackwell Science Ltd