The digestive system of sea spiders (Pycnogonida) presents peculiarities that have not been discussed in the context of their ecology or feeding behaviour. We investigated the digestive system of two Mediterranean species, a carnivorous species Ammothella longipes and a detritivorous Endeis spinosa, with special focus on its correlation with behavioural feeding habits. The midgut and hindgut sections did not present significant differences between the two species, but major differences were observed in the foregut, reflecting concordance to their diet and their feeding behaviour. Jaws, setose lips, the structure of the pharyngeal filter and musculature of the proboscis are the main differential elements when comparing feeding habits of A. longipes and E. spinosa. These elements are responsible for the reduction of the food pulp down to subcellular size. The digestion process observed in the species studied agrees with that observed in other pycnogonid lineages, but differs from most marine arthropods mainly because of the absence of midgut gland cells and the presence of a unique multifunctional type of midgut epithelial cell. Epithelial digestive cells are present in a small ‘resting’ form during starvation periods. During digestion, secretion granules possibly containing zymogen move to their apical border to be secreted to the midgut lumen, secondary lysosomes are formed and intracellular digestion occurs within them. Residual bodies are formed within the epithelial cell and released to the midgut lumen to be transported towards the hindgut. The characteristics of the digestive process of the pycnogonids studied seem to reflect a plesiomorphic state in arthropods.