Near infrared spectroscopy (NIRS) has been used in various applications such as food science, pharmaceuticals, agriculture, wildlife sciences, conservation and in fisheries. In fisheries it is extensively used for ageing and species differentiation through otolith. NIRS is also utilized to study the various aspects of fish or aquatic science such as evaluating the quality, fat, moisture and protein content, freshness of fish fillets, quality control, protein and energy digestibility, and ingredients in feed. NIRS is rapid, non-invasive, and inexpensive tool and has been used in several live animals to discriminate the biological sex, species, physiology, disease of animals. However, the feasibility of the NIRS to study the live fish is yet to be determined. In this preliminary study, the main objective was to understand and develop an attainable model to discriminate the species of the catfish which can only be differentiated through molecular technique. Channel and blue catfish ~750-800 gm was used for this study. Spectra from the 20 fish of each species were collected in three different methods: without anesthesia, with anesthesia (MS-222, 100mg/ml immersion) and gavage technique (2gm MS-222, 4gm NaHCO3/L). Head, region above the swim bladder around the lateral line and vent were used. Linear discriminant analysis (PCA-LDA) with the use of the wavelength from 700-1300 nm gave the better prediction model compared to the full NIR range (700-2500nm). Based on the prediction accuracy head had a better outcome (>80%) in all the different methods than other two regions. The major outcome of the study was the understanding the feasibility of NIRS in live catfish and creating the model. The model developed to study and differentiate live catfish can be used further to study the physiology, biological sex, species, health status of catfish.