Recent reports have demonstrated a cost associated with intersexuality in Amphipoda, including reduced fecundity and fertility. In this study, the gross morphology of the gonads in normal and intersex Echinogammarus marinus (Amphipoda) were compared to determine whether resource allocation to gonadal tissue accounted for this reduced fitness. Evidence for the presence of the male sex-determining hormone, androgenic gland hormone (AGH), was compared between sexual phenotypes using MALDI mass spectrometry. Two distinct intersex phenotypes (male intersex and female intersex) were found, with variation in gonadal structure corresponding with external phenotype. Examination of male intersexes revealed normal testicular development (testes, seminal vesicles and vas deferens), but also revealed the formation of an oviduct. Ovaries of intersex females showed normal ovarian development, but were reduced in length by approximately 20% due to the presence of vas deferens. The number of vas deferens in intersex females was equal to the number (one or two) of genital papillae. We hypothesise that the reduced ovarian length observed in intersex females is a likely cause of the reduced brood size previously reported in intersex females of this species. Variation in the sexual phenotype corresponded both to development of the androgenic gland and to expression of a peptide fragment corresponding to the A chain of androgenic gland hormone (AGH). Androgenic glands and a putative AGH peptide were present in males. However, in both normal and intersex females, the androgenic glands were only present in a rudiment form and the peptide was not detected. Intersex males were found to possess abnormal glands that appeared hypertrophied. However, AGH peptides were not detected, supporting the suggestion that the intersex phenotype is manifested via perturbations of AGH.