In bacteria, gene conservation and experimental data show that Lactococcus lactis has the simplest version of protein secretion system compared to Escherichia coli and Bacillus subtilis whose systems are more complex. L. lactis only possess the signal recognition particle (SRP) pathway, where the specific interaction of Ffh and FtsY is known to be essential for the efficiency and fidelity of its protein targeting. Therefore, modelling and structural characterization study of Ffh and FtsY will give an idea of its crucial region and amino acids that are critical in Ffh-FtsY interaction during protein targeting. This work is the first attempt to model L. lactis Ffh-FtsY complex, which was derived by computational docking, where a blind dock was applied. Results showed that the complex interface was predominantly stabilized by four hydrophobic interactions and 17 hydrogen bonds, where these putative binding interfaces are mostly confined at the motifs II and III in each G domain of Ffh and FtsY. Several residues were expected to play important roles in initiating or regulating guanosine triphosphate hydrolysis, including residue R142. This structural information will allow for the rational design of L. lactis Ffh-FtsY association in the future.