Abstract: To estimate the effects of Microcystin-LR (MC-LR) on the autophagy, we cloned Beclin1 CiBeclin1 gene from grass carp (Ctenopharygodon idella) using rapid amplification of cDNA ends (RACE) based on the EST sequence. The deduced amino acid sequence of CiBeclin1 was comprised of 447 amino acids, and CiBeclin1 possessed a typical Bcl-2 homology domain 3 (BH3) and an evolutionarily conserved domain (ECD). The similarity of CiBeclin1 amino acid sequence with other species was 88%—98%, and phylogenetic analysis demonstrated that CiBeclin1 formed a clade with rare minnow Beclin1. CiBeclin1 was ubiquitously expressed in 10 tested tissues, including the liver, kidney, spleen and others, with the highest level in liver. MC-LR significantly decreased the expression of CiBeclin1 at 24, 48, 72 and 96h, indicating that CiBeclin1 gene might play a regulatory role against MC-LR toxicity. However, whether the used doses of MC-LR could induce liver autophagy needs further investigation.