We investigated genotype of penicillin-binding protein (PBP) genes and macrolide resistant genes, the serotypes and the susceptibility to antibacterial agents against 258 strains of Streptococcus pneumoniae isolated from medical facilities in Gifu and Aichi prefectures between January 2010 and March 2011. These results were compared with those against 377 strains of S. pneumoniae isolated in 2008-2009. The number of genotype penicillin-susceptible S. pneumoniae (gPSSP) with 3 normal PBP genes, genotype penicillin-intermediate S. pneumoniae (gPISP) with 1 or 2 normal PBP genes and genotype penicillin-resistant S. pneumoniae (gPRSP) with 3 abnormal genes was 11 (4.3%), 135 (52.3%) and 112 (43.4%) strains, respectively. The isolates with no macrolide-resistant gene, only mefA, only ermB, and both mefA and ermB were 17 (6.6%), 65 (25.2%), 143 (55.4%) and 33 (12.8%). The prevalent pneumococcal serotypes isolated from children were type 19F (18.2%), following by type 6A and 15 (11.7%). The potential coverage of pneumococcal conjugate vaccine (PCV7) was 43.8%. The prevalent pneumococcal serotypes isolated from adults were high in order of type 19F (12.8%), type 6A, 3 and 11 (10.3%), excepting non-typable strains (17.9%), and from elderly persons were type 6B (23.2%) and type 3 (13.4%). The MIC90 of each antibacterial agents was as follows; 0.0625 microg/mL for garenoxacin, 0.125 microg/mL for panipenem, 0.25 microg/mL for imipenem, doripenem, tosufloxacin, 0.5 microg/mL for cefditoren, meropenem, moxifloxacin, 1 microg/mL for amoxicillin, clavulanic acid/amoxicillin, cefteram, cefcapene, ceftriaxone, 2 microg/mL for benzylpenicillin, piperacillin, tazobactam/ piperacillin, pazufloxacin, levofloxacin, 4 microg/mL for cefdinir, flomoxef, 16 microg/mL for minocycline, > 64 microg/mL for clarithromycin, azithromycin and these MIC90s were about the same as those in 2008-2009.