Abstract The distribution and origin of non-aromatic hydrocarbons (NAH) and polycyclic aromatic hydrocarbons (PAH) were investigated in surface sediments from the lagoons of ‘Grand Cul-de-Sac Marin’ and ‘Petit Cul-de-Sac Marin’ in the Caribbean island of Guadeloupe (61°30′W, 16°N). Both are surrounded by a mangrove ecosystem. Hydrocarbons extracted from sediments were fractioned by chromatography adsorption and analysed by gas chromatography. NAH concentrations ranged from 28.2–4104.4 μg g −1 of dry sediment and from 103–1656.5 ng g −1 for PAH. We founded that naturally occurring hydrocarbons predominated along the coastline. The harbour zone's sediment is polluted by petroleum hydrocarbons. PAHs in sediments are medium and high molecular weight residues with a pyrolytic origin.