Presence of nitrofuran and chloramphenicol in farmed prawn and shrimp is a major concern in the export sector of Bangladesh. Rejections of consignments by the foreign buyers have been recurrent for the last couple of years due to detection of these banned antibiotics. The increasingly complex requirements for food safety assurance and traceability set by major export markets represent a threat to the trade of this significant sector. In this study, the status and trends of the presence of nitrofuran and chloramphenicol in freshwater prawn Macrobrachium rosenbergii (De Man) and marine shrimp Penaeus monodon (Fabricius) and in their feeds in the Southwest coastal region of Bangladesh were investigated. The prawn/shrimp farmers, feed manufacturers and feed sellers were interviewed with well structured pre-tested Questionnaires. Antibiotic residues present in the animal muscles, feeds and feed ingredients were detected using LC–MS–MS by the Fish Inspection and Quality Control Wing of the Department of Fisheries. The study reveals that farmers did not deliberately use those banned antibiotics, but these chemicals were detected in many M. rosenbergii and P. monodon samples in 2008, 2009 and 2010, in both fresh muscles, pre-export and post-export consignments. The percentage of contamination with this banned antibiotics in M. rosenbergii samples were 17.74%, 22.89%, 13.60% and in P. monodon samples were 12.65%, 15.79%, 11.85% in 2008, 2009 and 2010 respectively. Antibiotic residue data of 2008, 2009 and 2010 showed: (i) contamination of nitrofuran and chloramphenicol was more in M. rosenbergii than P. monodon; (ii) among four nitrofuran metabolites, nitrofurazone was found more frequently but in smaller quantities in 2009 and 2010; (iii) contamination of nitrofuran metabolites was more in prawns fed with commercial feed than those with home-made feed; and (iv) there has been a decreasing trend of the presence of nitrofuran and chloramphenicol in prawn and shrimp of Bangladesh.