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Microbes are the most significant ubiquitous pathogens that cause serious infections in freshwater fish, leading to tremendous economic losses. The present study was designed to investigate the extent of changes in cytokine expression, hemato-biochemical parameters, and tissue histology of <i>Cirrhinus mrigala</i> (<i>C. mrigala</i>) challenged with <i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) and <i>Fusarium oxysporum</i> (<i>F. oxysporum</i>). Fish were divided into three major groups: control, <i>P. aeruginosa</i>-challenged, and <i>F. oxysporum</i>-challenged. The infection in both challenge assays was allowed to progress until 7 days post infection. Upregulated expression of <i>TNF-α</i> and <i>IL-1β</i> was found in blood, gills, livers, and kidneys of the challenged fish. Significant differences were noted in hematological parameters of challenged fish. Alanine aminotransferase, aspartate aminotransferase, and alkaline aminotransferase levels also showed significant differences in infected and control groups. An increase in serum albumin and globulin and a decrease in total protein were noted in infected groups as compared to the control group. Severe histological alterations were noted in gill, liver, and kidney tissues of the infected groups as compared to control. The order of histological alteration index for <i>P. aeruginosa</i> challenge was liver > kidney > gills, and for <i>F. oxysporum</i> challenge it was kidney > liver > gills. These changes in fish infected by <i>P. aeruginosa</i> and <i>F. oxysporum</i> can be used as an effective and subtle index to monitor the physiological and pathological conditions of fish.