In vertebrates, the T cell receptor (TCR) plays a crucial role in immune system. To date, the roles of fish TCRs in response to pathogen infection are still poorly understood. In the present study, we firstly cloned and identified the TCRα and TCRβ from dojo loach (Misgurnus anguillicaudatus) by RACE approaches. The full-length cDNAs of Ma-TCRα and Ma-TCRβ include an open reading frame (ORF) of 723 and 879 bp encoding a polypeptide of 241 and 293 amino acids, respectively. Structural analysis indicated that Ma-TCRα and Ma-TCRβ had a signal peptide, IgV domain, IgC domain, a connecting peptide (CPS), a transmembrane region (TM) and a cytoplasmic (CYT), which are similar to their counterparts described in other teleost. Phylogenetic analysis supported that Ma-TCR Cα and Ma-TCR Cβ were closely related to the Cα and Cβ region of Cyprinidae family, respectively. Transcriptional expression analysis indicated that Ma-TCRα and Ma-TCRβ mRNAs were ubiquitously expressed in a wide array of tissues and most abundantly found in skin, brain, kidney, gill and spleen. The expression patterns of Ma-TCRα and Ma-TCRβ after bacteria (F. columnare G4), parasite (Ichthyophthirius multifiliis) and fungus (Saprolegnia) infection were detected by qRT-PCR. Additionally, the morphological changes of gill and skin following the three infection models were investigated. The results clearly indicated that Ma-TCRα and Ma-TCRβ was significant up-regulated not only in spleen and kidney, but also in skin and gill. In summary, our present findings suggested that Ma-TCRα and Ma-TCRβ might play significantly roles in the modulation of immune response and protect loach from different pathogens infection.