Smoking is the most widely practiced method applied practically for all species of fish. Smoking is a technique for preserving fish that has been processed with organic components derived from smoke. Smoke produces volatile fragrant compounds that impart specific properties to fish flesh. Fish smoking commonly takes place in conventional kilns with direct burning of wood, sawdust, coconut shell and coal combustion at high temperatures. The heat burnt organic matter may release chemical contaminants, polycyclic aromatic hydrocarbons (PAHs) via the pyrolysis process, leading to PAHs contamination in smoked fish. Therefore, this research is carried out to investigate the impact of smoking materials (wood and charcoal) on the quality of smoked fish (Clarias microcephalus) and levels of PAH contamination. The moisture content of smoked fish using wood and charcoal were below 6%. Smoked fish using charcoal tended to have higher ash content, protein and lower total fat than smoked fish using wood. The result of peroxide values of smoked fish using wood and charcoal were 15.19 ± 0.69 meq/kg and 8.45 ± 0.51meq/k, respectively. TBARS value were 3.76 ± 0.36 mg MDA/kg and 3.68 ± 0.1 mg MDA/kg for smoked fish used wood and charcoal, respectively. The results of PAH analysis, BaP and ∑PAH4 concentrations exceeded the maximum limit set by the Regulation Commission European Union (EU) 1881/2006 of 2 µg/kg and 12 µg/kg, respectively. BaP containing in smoked fish with skin was 3 to 4 times higher by comparison to smoked fish without skin, while ∑PAH4 of smoked fish with skin was 2 to 3 times higher. The concentration of BaP and ∑PAH4 in smoked fish using wood was higher than smoked fish using charcoal. As conclusion, smoked fish should be consumed with skin removal and smoke with charcoal as a heat resource in order to reduce PAH contamination. The design of the smoking kiln and the adjustment of the smoking process could be considered in further study to ensure smoked fish quality and to mitigate the health issues for consumers.