We evaluated the possibility of isolating DNA from environmental samples to detect and identify invasive fish species based on variation in the sequences for mitochondrial gene region. Goldfish CO1 DNA was successfully amplified from the water in a tank containing goldfish. Sequencing results verified that the DNA extracted from water matched goldfish sequences obtained from DNA extracted from tissue from other sources. We also evaluated the potential of a DNA-based system to detect and identify invasive fish species based on difference in the length of several gene regions. Sequences for the 12S and 16S rRNA genes, cytochrome c oxidase subunit 1 (CO1) gene and the d-loop region downloaded from GenBank suggested that sequences from these genes would contain enough variation to distinguish six pest fish species (koi carp, rudd, brown bullhead catfish, goldfish, perch and gambusia) introduced to New Zealand freshwaters. A 250-nucleotide region of the 16S rRNA gene was successfully amplified and sequenced from fish tissue, faecal material and fish mucus. While sequences from these regions could distinguish fish species, there was insufficient variation in length to identify each fish species. Future directions for this research are suggested.