Abstract: In order to verify whether the cryptochrome protein IgCRY1 of Isochrysis galbana interacted with the downstream protein IgCOP1, the total RNA of Isochrysis galbana was extracted and reverse transcribed into cDNA as a template to amplify the target fragment. The BD-IgCRY1 and AD-IgCOP1 vectors were constructed and co-transfected into the yeast strain AH109 for the yeast two-hybrid verification. And the bioinformatics analysis of IgCOP1 protein was performed. The results showed that the CDS sequences of IgCRY1 and IgCOP1 cloned from Isochrysis galbana were 1 560 bp and 1 185 bp, respectively. The mutual interaction between IgCRY1 protein and IgCOP1 protein was verified by the yeast two-hybrid system. The bioinformatics analysis of the interacting protein IgCOP1 revealed that the molecular size of the protein was 43.7 kDa, and the number of encoded amino acids was 394, which was a typical hydrophilic protein with 62.69% of its secondary structure irregularly coiled. The phylogenetic tree analysis showed that IgCOP1 protein was clustered at the bottom of the branch, and had a distant relationship with the other branches. The verification of the interactions between IgCRY1 protein and IgCOP1 protein provided an important theoretical basis for the biological process of light signal regulation in Isochrysis galbana.