This study gives a first qualitative and quantitative record of the parasitic infracommunities in two deep-sea fish species inhabiting the locality of the Juan Fernández Archipelago, Chile. In December of 2002 a total of 12 individuals of Coelorynchus chilensis and 35 Notacanthus sexspinis was obtained as by-catch of a shrimp Haliporoides diomedeae fishery at around 1000 m depth. The majority of the individuals of both species were infected at least by one parasitic taxon. Forty-five parasites were collected from C. chilensis including larval cestodes, Hepatoxylon trichiuri, Grillotia sp., larval nematodes Anisakis sp., adult digeneans Dinosoma sp., Brachyphallus sp., copepods Protochondia cf. longicauda and myxozoa Myxidium sp. Twenty-two parasitic individuals were collected from N. sexspinis belonging to adult digeneans Lecithochirium sp., and Accacladium sp. (without eggs, immature), larval cestodes Hepatoxylon trichiuri, larval nematodes Anisakis sp. and myxozoa Ceratomyxa sp. Most of the parasites showed a low prevalence and abundance in both host species, except for Myxidium sp., Ceratomyxa sp., Dinosoma sp. and Brachyphallus sp. The parasites Hepatoxylon trichiuri and Anisakis sp. were the only shared taxa. These infracommunities are low in richness, diversity and abundance compared to shallow water fish–parasites communities. Nevertheless the numeric properties of infracommunities are not reliable due to sample size. Given the additional difficulties with reliable sampling of deep-sea fish, these results should not have too much significance attributed to them. The relevance of this study is simply the recognition of parasites that infect the deep-sea fish of the families Macrouridae and Notacanthidae in the southern hemisphere.