Chikungunya (CHIK) disease caused by mosquito transmitted Alphavirus. Chikungunya showed worldwide epidemics including some fatal cases. Thus there is need for a safe and effective therapy for Chikungunya. In this study we delineated linear dominant B and T cell epitopes of envelope E1 and nucleocapsid proteins with neutralizing potential in vitro. Immunogenicity of synthesized peptides, encapsulated in PLGA micro particles was done intramuscularly with CpG ODN as adjuvant in outbred and inbred H-2d mice. Few peptides showed high antibody peak titer with robust memory response. Peptides of E1 and Capsid proteins showed antibody peak titer in ranging 1,18,000 to 2,40,000. Peptides E1P1, E1P4, E1P10 of E1 protein and CP3, CP5, CP9 of capsid protein were found major B cell epitopes. E1P4, E1P9 and CP6 peptides were identified as T cell epitopes, confirmed by T cell lymhoproliferation assay and cytokines profile. Peptides E1P4, E1P9 and CP6 induced Th1 and Th17 type of immune response. During antibody isotyping E1P1, E1P4, E1P10, CP3, CP9 peptides showed equal distribution of IgG1, IgG2a and IgG2b subclass. More importantly E1P1, E1P4, E1P10, CP3 & CP9 peptide specific antibodies showed in vitro neutralization (>90%) to CHIKV in plaque reduction neutralization test (PRNT90). Overall identified epitopes can be assembled in multiple antigenic peptides (MAPs) for developing effective subunit vaccine for CHIKV.