Effect of smoking technologies on nutritional quality and concentration levels of polycyclic aromatic hydrocarbons (PAHs) in Mormyrus caschive and Oreochromis niloticus were determined to enable adoption and utilization of suitable facility that maintains good quality for sustainable supply of nutritious fish products in South Sudan. A total of 72 fresh M. caschive and O. niloticus were purchased, of which 24 were iced for reference and the other 48 were divided into two groups for pit and chorkor smoking. Experimental smoking of fish samples was conducted twice in a randomized design. Fish samples were analyzed for nutritional values using standard methods of the association of official analytical chemists and levels of PAHs using gas chromatography-mass spectrometry. Results revealed; the two smoking methods concentrated crude protein, fat and ash contents. However, fish smoked using chorkor had significantly higher nutritional values than fish smoked using pit kiln. About seven types of PAHs comprising of low and medium molecular weight were recorded from the two smoked fish species. Naphthalene and fluorene were the two dominant PAHs with fish smoked using pit kiln having significantly higher concentration levels of naphthalene (5.86±4.16 µg/kg) and fluorene (3.83±0.10 µg/kg) than fish smoked using chorkor oven. The study concluded that chorkor oven has better quality smoked fish than pit. Hence, its utilization and adoption for artisanal fisheries in South Sudan is recommended.