The International Seabed Authority is responsible for protecting the deep-sea environment from damage and excessive exploitation. To succeed in this task, procedures and guidelines have to be implemented for the establishment of environmental baselines. Nematodes are the dominant animals of the potential mining regions; they can make up between 50 and 90 per cent of the measurable deep-sea fauna. Clearly, any monitoring of industrialisation of the deep sea will involve nematode identification. However, marine nematode taxonomy is woefully underdeveloped. Few species outside of the North West European continental shelf have been described and most descriptions are poor and rely on superficial characters.Nematode identification using traditional morphological methods and light microscopes is difficult, time consuming and expensive. Recent molecular research has raised doubts about whether the traditional morphological characters used are adequate to distinguish sibling species or those demonstrating convergent evolution. There are insufficient traditional marine nematode taxonomists to undertake an extensive deep-sea monitoring campaign, and training new experts would be an extraordinarily slow and expensive business. New molecular technology offers the potential of a cheap, fast and, more importantly, objective way of identifying deep-sea nematodes. Furthermore, molecular identification, or ‘barcoding’ to use the jargon, does not require taxonomic expertise but uses more widely distributed technical skills.This document is a practical guide for undertaking a molecular survey of deep-sea nematodes including protocols for collecting deep-sea nematodes, preservation and shipping of samples, slide mounting, image capture and the production of individual molecular barcodes. New technologies are discussed such as microarray-based identification systems and massively parallel sequencing (MPS). These future developments could conceivably be integrated into the system presently proposed for even faster and more accurate results.