The invention discloses an agarase and an acquisition method of an encoding gene thereof. The acquisition method utilizes various PCR methods to acquire the agarase gene aga41 from marine bacteria vibrio natriegens (the preservation number is CGMCC No.2428) for the first time and breaks through the conventional method which screens the agarase gene by constructing a library. The agarase gene aga41 belongs to a GH50 family in a beta-agarase. The whole length of the agarase gene aga41 is 2,973bp. 990 amino acids are encoded on the agarase gene aga41. The highest sequence similarity of the agarase gene aga41 with the existing agarase is 49 percent. The agarase gene aga41 is a novel beta-agarase. An activated recombinant agarase which is obtained by cloning the agarase gene of the invention on an expression vector pET28b, constructing a recombinant escherichia coli Rosetta bacterial strain and carrying out heterologous expression can be applied to the industrial production.