We used four pairs of polymerase chain reaction primers complementary to the ends of interspersed nuclear elements to amplify markers that differentiate bull trout (Salvelinus confluentus) and brook trout (S. fontinalis) and allow the identification of hybrids between these species. We identified 21 DNA fragments in bull trout that are absent from brook trout and 13 DNA fragments in brook trout that are absent from bull trout. This PCR-based test gave results that are consistent with results from allozyme loci known to be diagnostic for these species. Similar interspersed elements are found in all eukaryotes, making this a potentially useful technique for species identification in many taxa.