Organisms have naturally build defense mechanisms against infections and diseases caused by pathogens. This system known as immune system comprises of innate immunity and adaptive immunity. Innate immunity is non specific and produces a quick response to the invading pathogens. Macrophages play central role in innate immunity, also called natural immunity. The other part of immunity is rather specific and it takes some time to show its response, this type of immunity is called adaptive immunity. Adaptive immunity can be either T cell mediated or B cell mediated in response to intra cellular or extra cellular pathogens respectively. When it is T cell mediated it will lead to the secretion of cytokines including interferon along with other substances, which help to fight intra cellular pathogens especially viruses by activating natural killer cells and macrophages. B cell mediated immune system leads to production of antibodies in response to extra cellular pathogens in blood or other body fluids. The whole immune system including innate immunity and adaptive immunity mediated by both T cell and B cell are not separate from each other but rather linked with each other and activating each other against foreign invaders. For example macrophages activate T cells, T cells activate macrophages, B cells and other T cells. Purpose of present study is to know about the adaptive immune system of two farm fishes, rainbow trout and common carp which are main source of protein in Pakistan. This study will provide a guide line to improve the immune system of farm fishes so that they can be resistant to diseases. This will ultimately benefit the human beings as they will get more Omega 3 rich protein, which is good for the over all health of human beings. In the present work both cellular and humoral aspects of adaptive immune system mediated by T and B lymphocytes were studied. Two teleost fishes rainbow trout Oncorhynchus mykiss (Scottish farm fish) and common carp Cyprinus carpio (Pakistani farm fish) were taken as experimental animals. Immune genes which regulate interferon production as a cellular immune response to viruses or other intracellular pathogens, werestudied in rainbow trout Oncorhynchus mykiss, B cell mediated immune system leading to production of antibodies was studied in common carp Cyprinus carpio. It was found that production of interferon is regulated by immune genes known as interferon regulatory factor (IRF) genes. These IRF genes are 10 in number and are named as IRF1, IRF2, IRF3, IRF4, IRF5, IRF6, IRF7, IRF8, IRF9& IRF10 and altogether form IRF family. IRF genes have been sequenced so far in many species including human beings. In rainbow trout IRF1, 2, 3&7 have been sequenced till to date. In present project work was done on remaining members of the IRF family. During the project two full length genes IRF 4& IRF8 were sequenced along with partial sequences of IRF 5& IRF10. It was found that certain toxicants like Poly I: C trigger IRF genes to produce positive immune response by secreting cytokines like interferon. Poly I: C (Polyinosinic: polycytidylic acid) is a synthetic double-stranded RNA that is used experimentally to model viral infections in vivo. IRF4 gene was expressed in rainbow trout spleen cells treated with Poly I: C for 4 hours. IRF 8 gene was expressed in spleen and head kidney cells. After multiple alignments of genes it was found that the gene structure of IRF4&8 genes found in rainbow trout had close structural resemblance with IRF4&8 genes found in other fish like zebra fish or even in mammals like human being and mouse. IRF4 &IRF8 play an important role in maturation of B and T lymphocytes. The other aspect of adaptive immune system, B cell mediated or humoral immunity was studied in common carp Cyprinus carpio. It was found that humoral antibodies are detected in serum of fish after secondary immunization with particulate antigen SRBC (sheep red blood cells). Proliferative response in lymphoid tissues especially in spleen and kidney was high while there was less response in liver. HGG localization in these tissues was studied by using fluorescent labeled antibodies against HGG. Farm fish in Pakistan are built in agricultural lands and so these fish are in contact with the pesticides used on crops through water run off to these fish farms. It was found during experimental work that toxicants like pesticides affect the immune system of common carp by suppressing the production of antibodies. Histological studies were also conducted which showed that besides affecting immune system of fish, these pesticides also have harmful affects on lymphoid tissues of fish and also on immune system of fish.