In the present study, magnetite nanoparticles with amine functional groups were synthesized successfully, and were characterized by TEM, XRD and Raman spectroscopy. The size and shape of the amine functionalized magnetite nanoparticles as characterized by TEM, were in the size range of 13-14 nm with spherical shape. The composition and phase purity of magnetite nanoparticles such as crystal phase, particle size and magnetic properties as determined by XRD, showed that the crystal structure formed is corresponding to Fe3O4 nanoparticles. The results obtained from the Raman spectrum showed the presence of magnetite with amine groups. Ligand coupled magnetic nanoparticle affinity matrices were developed successfully by coupling the Fe3O4 magnetic nanoparticles to phosphomannan (PMC) oligosaccharide and lactose separately using DVS as the spacer arm. The Fe3O4-phosphomannan matrix specifically can bind the Cation Dependent mannose 6-phosphate receptor (CD-MPR) and can be eluted using mannose 6-phosphate. The eluted protein migrated as a single band in SDS-PAGE under reducing conditions corresponding to molecular mass of 46 kDa and was recognized by MSC1 antibody. Lactose-specific lectin (LSL) from Lamellidens corrianus binds specifically on Fe3O4-lactose matrix and can be eluted using 0.3 M lactose. The eluted LSL migrated as a three subunit species with molecular masses of 34 kDa, 30 kDa and 25 kDa under reducing conditions in SDS-PAGE. The three subunits were recognized by a LSL-polyclonal antiserum. These new matrices developed offer a great advantage in the purification of lectins (MPR 46 and LSL) from animals over conventional ligand-coupled Seralose matrices.