Gene encoding mannan-binding lectin serine protease (MASP) plays an essential important role in innate immune response of host, especially in activation of complement system via the lectin and alternative pathways. MASPs family consisted of three distinct genes (MASP1, MASP2 and MASP3). Therefore, the current study aimed at sequencing AcDN and analyzing molecular structure of the MASP3 (MASP1 isoform 2). With 2,657 bp and 11 exons, in which the coding region is from nucleotide nt. 152-2388, MASP3 encoded 728 amino acids. There was high homology among mammalian species (pig, human, cattle and dog) at both cDNA (87-90 percent) and protein (92-94 percent) levels. Macromolecule MASP3 had 27 cysteine residues. However, amino acid with high percent in its protein included Ser (8.4 percent), Val (8.1 percent), Leu (8.0 percent), Gly (7.6 percent) and Glu (7.1 percent). With a molecular mass of approximately 81.55 kilo Daltons, MASP3 was an assembly of richysteine protein domains such as CUEl (a.a 18-138,2 cysteine), EGF_CA (a.a 139-182, 6 cysteine), CUB2 (a.a 185-297, 3 cysteine), CCP1 (a.a 301-362, 4 cysteine), CCP2 (a.a 367-432, 4 cysteine) in Nterminus and Tryp_SPc (a.a 449-711, 5 cysteine) in C-terminus. The Tryp_SPc is the largest domain whereas EGF_CA is the smallest. Besides those, a signal peptide (a.a 1-19), 13 disulfide bonds, 5 Nglycosylation sites, and methionine loop (a.a. 630-649) were also identified. These are as major premises for further studies for roles of the MASP3 in immune response mechanism for disease resistance in pigs.