Until now, the H1N1, H1N2, and H3N2 subtypes were mostly circulating in swine populations within swine-raising countries including Korea. The pandemic (H1N1) 2009 (pH1N1) infection was detected in April of 2009, and spread quickly from person to person on a global scale. This study was performed to investigate the dynamic fluctuations of innate lymphoid cells, T cells, dendritic cells (DC), and natural killer (NK) cells in the spleens of mice infected with two reassortant H1N2 viruses (strain C7 and E34), swine-derived endemic H1N2 virus (strain 100-4), and one pH1N1 virus (strain J2). The relative numbers of T cells, NK cells, and DC in the spleen were determined at 2, 5, and 9 days post-inoculation (dpi) by flow cytometry. Serum cytokines were examined in parallel by enzyme-linked immunosorbent assay. NK, DC, CD4+, and CD8+ cell numbers and IFN-γ levels were increased in mice infected with strain 100-4 until 5 dpi and then decreased at 9 dpi, whereas strain J2 and the two reassortant H1N2 viruses carrying three (PB2, M, and NS; strain C7) or four (PB2, PA, M, and NS; strain E53) genes from pH1N1 had the opposite effect. The frequency of CD8+ Treg cells and IL-6 levels was up-regulated in by strains J2, C7, and E34, but not in strain 100-4. The serum cytokines IL-2 and IL-4 were not significantly affected by any strain up to 9 dpi. Our results indicate that novel reassortant H1N2 virus causes effects on the innate lymphoid population similar to the effects of the pH1N1 virus. Further studies are required to verify the relationships among the genes of each strain and bio-pathogenicity in other mammalian species.