Small indigenous fishes are good source of micronutrients and omega 3 fatty acids for human being. They are harvested at a large amount, but since they are extremely perishable food item, a small fraction of it is sold at fresh condition and rest has to be preserved i.e., either by freezing or drying and sold at low price. The ethnic people of North east India, consume them in both their fresh and preserved form, without having much knowledge about its nutritional status. Hence, an investigation was done to find out the nutritional change in terms of mineral content and polyunsaturated fatty acids during their preservation period. The fatty acid and micronutrient content was estimated in six small indigenous fishes altogether in fresh, frozen and sun-dried state. The sample fishes were-Amblypharyngodon mola, Chanda nama, Esomus danricus, Mystus tengara, Puntius sophore and Trichogaster fasciata. In all the three states, fatty acid content was estimated by GCMS and micronutrient content was estimated by AAS. Results showed that there is definite impact of preservation in the nutrient values of small indigenous fishes. Freezing increased the value of certain essential fatty acids i.e. EPA, DHA, Arachidonic acid, Vaccenic acid and Oleic acid. In case of micronutrients the impact of freezing was negligible, since values decreased insignificantly. The sundried fishes showed higher nutritional value in both the micronutrient content and fatty acid content than the fresh and frozen fishes. It was observed that fatty acid content and microenutrient do not get deteriorated during a short term freezing period however, sun dried conditions enhances the nutritional content in terms of fatty acids and micronutrient quality of the small indigenous fishes of Assam.