Heat shock proteins (HSPs) are highly conserved molecular chaperones that play critical roles in both innate and adaptive immunity. However, little information about HSPs from marbled eel Anguilla marmorata is known. In this study, the full-length Amhsp90 (2527 bp), Amhsp70 (2443 bp) and Amhsc70 (2247 bp) were first cloned from A. marmorata, using rapid amplification of cDNA ends, containing open reading frames of 2181, 1932 and 1950 bp in length, and encoding proteins with 726, 643 and 649 amino acids, respectively. The deduced amino acid sequences of three Amhsps shared a high homology similarity with other migratory fish. Real-time fluorescent quantitative polymerase chain reaction was used to evaluate tissue-specific distribution and mRNA expression levels of three Amhsps subjected to infection with Aeromonas hydrophila. The mRNA expression of three Amhsps in eight tested tissues, namely liver, heart, muscle, gill, spleen, kidney, brain and intestine, of juvenile A. marmorata was evaluated to reveal the major expression distribution in liver, intestine, muscle and heart. After pathogen challenge treatments, mRNA transcriptions of three Amhsps revealed a significant regulation at various time points in the same tissue. All these findings suggest that Amhsps may be involved in the immune response in A. marmorata.