Representational difference analysis (RDA), a technique for the isolation of differences between highly similar complex genomes, was employed for isolation of species-specific markers. These markers can be easily adapted for a high throughput PCR-based assay in which multiple specimens can be simultaneously identified based on the presence/absence of amplification products. One of the important features of RDA performed on genomes of different species (interspecific RDA) is its ability to preferentially isolate families of repetitive sequences that are unique to one of the compared genomes. Such families of repetitive DNA are homoplasy-free characters that can be used for cost-efficient, mass identification of specimens in a variety of situations ranging from mark-recapture studies to screenings of egg or larval stages.