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Application of good sanitation practice in cryopreservation process is the key issue to improve the quality of cryopreserved fish sperm. This study implemented standard sanitation protocol with minimal contamination and evaluated the source of bacterial contamination associated with laboratory equipment and related materials across a series of cryopreservation process of silver barb (Barbodes gonionotus) semen. The use of 16s rRNA sequencing and traditional biochemical methods were performed for bacterial identification. Animal origin (anal fin, culture water and semen contaminated with faeces and urine) and non-animal origin (liquid nitrogen from liquid nitrogen dewar, outer surface of straw, air circulation in cryopreservation laboratory and latex gloves used during cryopreservation procedure) were determined for bacterial contamination. Aeromonas punctata subsp. caviae was the most abundant species in anal fin, latex groves and semen contaminated with faeces and urine. Bacillus safensis and Bacillus sp. were found as frequently recovered species from liquid nitrogen dewar. Aeromonas hydrophila subsp. hydrophila and Pseudomonas fluorescens, fish pathogenic bacteria, were isolated from all animal origin samples. This was the first report indicating that standard sanitation and hygiene methodologies are recommended for sperm cryopreservation of B. gonionotus to prevent bacterial contamination.