Genetic sampling and molecular investigations are important parts of studying wild populations. However, collecting tissues from free-ranging animals can be difficult or impractical. This study develops a sampling and extraction protocol for template DNA from faecal material collected in a marine environment from small cetaceans. DNA was extracted from faecal material of free-ranging Atlantic spotted dolphins (Stenella frontalis) and subsequently tested for its suitability in molecular investigations by amplifying both mitochondrial and nuclear DNA. The resulting mitochondrial sequences were found to closely match known S. frontalis haplotypes. Three microsatellite loci were amplified and fall within the expected size range for cetaceans. Mother and calf families previously assigned by observation were genetically confirmed using both mitochondrial haplotype and allele sharing between the mother and offspring. The protocol effectively collects and extracts dolphin DNA from faecal samples and enables species identification as well as confirmation of genetic relatedness and should be considered as a noninvasive alternative to current protocols.