Molecular identification and development of a novel recombinant alginate lyase as the biocatalyst for alginate saccharification are prerequisite for bioethanol fermentation from brown seaweed biomass. We identified and characterized a novel oligoalginate lyase for complete degradation of alginate from Stenotrophomonas maltophilia KJ-2 that grow on alginate as the sole carbon source. KJ-2 oligoalginate lyase consisted of AlgL- and heparinase II/III-like domains. The recombinant KJ-2 oligoalginate lyase exhibited substrate preference toward polymannuronate and alginate as well as oligoalginate. The recombinant KJ-2 oligoalginate lyase completely degraded alginate into unsaturated uronate monomer most efficiently at pH 7.5 and 37 oC. Interestingly, AlgL-like recombinant proteins showed more like endolytic activity. The recombinant KJ-2 oligoalginate lyase was a novel oligoalginate lyase consisting of AlgL- and heparinase-like domains and could be used as a candidate for biocatalyst selection to saccharify alginate for bioethanol production from brown seaweed.