In this study, site-directed mutagenesis was performed on the β-agarase AgaA gene from Zobellia galactanivorans to improve its catalytic activity and thermostability. The activities of three mutant enzymes, S63K, C253I, and S63K-C253I, were 126% (1,757.78 U/mg), 2.4% (33.47 U/mg), and 0.57% (8.01 U/mg), respectively, relative to the wildtype beta-agarase AgaA (1,392.61 U/mg) at 40°C. The stability of the mutant S63K enzyme was 125% of the wild-type up to 45°C, where agar is in a sol state. The mutant S63K enzyme produced 166%, 257%, and 220% more neoagarohexaose, and 230%, 427%, and 350% more neoagarotetraose than the wild-type in sol, gel, and nonmelted powder agar, respectively, at 45°C over 24 h. The mutant S63K enzyme produced 50% more neoagarooligosaccharides from agar than the wild-type beta-agarase AgaA from agarose under the same conditions. Thus, mutant S63K β-agarase AgaA may be useful for the production of functional neoagarooligosaccharides.