Formalin contamination in edible fishes is strictly prohibited in Bangladesh. Although studies reported formalin contamination in many different commercial large table fish’s items but research pinpoints the formalin contamination in Small Indigenous Species (SIS) of fishes are scant. The present study was aimed at detecting the presence of formalin in SIS from different fish markets of Sylhet Sadar Upazila, Bangladesh. Five SIS taxa explicitly Coricaso borna (Kachki), Amblypharyngodon mola (Mola), Gudusia chapra (Chapila), Mystus tengra (Tengra), Puntius ticto (Tit punti) were purposely sampled during winter season (November to December, 2014) and summer (May to June, 2015) from eight fish markets for the detection of formalin content by using formalin testing kit developed by Bangladesh Council of Scientific and Industrial Research (BCSIR). A total of 160 SIS individuals were collected, where 50 samples were contaminated with formalin in which 32 samples (40%) were in summer and 18 (22.5%) in the winter season. The rate of formaldehyde contamination was higher in C. soborna (100% both in summer and winter) followed by G. chapra (75% in summer and 12.5% in winter) and A. mola (50% in summer and 0% in winter) respectively. The formalin contamination was found statistically significant (P value <0.05) for Chapila and Mola in both season. It is, therefore, strongly recommended to ensure the institutional and government support and extension aids for improving the formalin testing methods, marketing systems and market facilities that can ensure a good quality fresh/safe fish in the markets for consumers.