To investigate the characteristics of Tc1/Mariner transposons in four catfish genomes (Ictalurus punctatus, Glyptosternum maculatum, Silurus asotus and S. meridionalis) and their role in the evolution, we used de novo and homology methods to predict Tc1/Mariner transposons and explored the role in the evolution of those four catfishes. The results showed that the contents of Tc1/Mariner transposons in the four catfishes were 9.46%, 2.70%, 7.83% and 8.54%, respectively. All the Tc1/Mariner transposons in the four catfishes were classified into 38, 20, 43 and 55 families, respectively. Based on the structural and phylogenetic analysis of the catalytic region of the transposase, the Tc1/Mariner transposons in the four catfishes can be classified into five different subgroups: Tc1 (DD34E), DD35E, DD36E, DD37E and pogo (DD35D). Phylogenetic analysis indicated that the transposons of most of the branches for S. asotus and S. meridionalis were clustered into sister groups. The results indicated that the insertion time of the majority Tc1/Mariner transposons mainly ranges between 0-5 Mya (million years ago). Many Tc1/Mariner transposons have a burst expansion between 0-1 Mya or 2-3 Mya. In addition, most of the Tc1/Mariner transposons in the four catfishes were inserted into the intron of the gene. In summary, this study provides new insights into the evolution of Tc1/Mariner transposons in the fish genomes.