Large-scale genetic sampling by non-invasive methods is of vital importance for the conservation of vulnerable or elusive species. In the marine environment, non-invasive genetic sampling can provide a powerful alternative to conventional biopsies. We designed and implemented mucus swabbing for a free-ranging elasmobranch, thereby demonstrating the utility of this method in the field. We report the first attempt at mucus collection from 30 plankton-feeding basking sharks Cetorhinus maximus from 3 spatially distinct ‘hotspots’ in Irish waters. C. maximus DNA was successfully extracted and verified using DNA barcoding of the mitochondrial DNA cytochrome c oxidase 1 gene (99% sequence similarity) and basking shark species-specific multiplex PCRs derived from the nuclear ribosomal internal transcribed spacer 2 locus. Mitochondrial control region sequencing (1086 bp) showed that Irish samples were dominated by 2 haplotypes previously found to be globally distributed. Additionally, 1 novel haplotype was defined from western County Kerry. On-going genetic tagging will eventually provide more accurate estimates of global basking shark population structuring, abundance and behavioural ecology.