Objective To study immunohistochemical localization of high mobility group protein N2(HMGN2) protein in porcine tissues, and evaluate the antimicrobial activity of its active domain, α-helical domain in vitro. Methods In this study, we investigated the localization of HMGN2 protein in porcine tissues using the immunohistochemical method. In addition, we isolated and purified HMGN2 from porcine thymus and lymph node by the high-performance liquid chromatography(HPLC), and then we synthesized α-helical domain of HMGN2. After that, we evaluated the antimicrobial activity of HMGN2 and α-helical domain of HMGN2, against Streptococcus mutans, Streptococcus sobrinus, Candida albicans and Escherichia coli in vitro. Results The results showed that HMGN2 could be isolated and purified from porcine thymus and lymph node, and all the tested porcine tissues were immunoreactive to HMGN2 proteins. The proteins mostly presented in the cytoplasm and nucleus. Synthetic α-helical domain of HMGN2 and HMGN2 had equivalent antibacterial activity, and both of them had potent antimicrobial activity against the selected bacteria and fungi. Conclusion The study suggested that the HMGN2 proteins mostly presented in the cytoplasm and nucleus in porcine tissues, and HMGN2 and synthetic α-helical domain of HMGN2 had potent antimicrobial activity against some bacteria and fungi.