In order to develop a microsatellite typing system for Lepeophtheirus salmonis (Krøyer), a DNA preparation method for individual sea lice suitable for analysis by polymerase chain reaction (PCR) was designed, and the DNA sequences of 50 L. salmonis microsatellite elements were determined. The microsatellites were composed of 60% perfect, 25% imperfect, and 15% compound repeats. Based on the flanking DNA sequences, four microsatellite‐PCR assays were optimized and used in a pilot study to analyse L. salmonis samples collected in Ireland, Norway and Scotland. Two of the microsatellite‐PCR assays targeted polymorphic loci amplifying seven and 10 alleles respectively. The results showed that microsatellite‐PCR typing could detect genetic variation both within and between the L. salmonis groups, and also was capable of amplifying group‐specific alleles.