Dengue is a severe emerging arthropod-borne viral disease occurring globally. Around two-fifths of the world’s population or up to 3.9 billion people are at a risk of dengue infection. Infection induces a life-long protective immunity to the homologous serotype but confers only partial and transient protection against subsequent infection against other serotypes. Thus, there is a need for a vaccine which is capable of providing a lifelong protection against all the serotypes of dengue virus. In our study, comparative genomics of Dengue virus (DENV) was conducted to explore potential candidates for novel vaccine targets. From our analysis we successfully found 100% conserved epitopes in Envelope protein (RCPTQGE); NS3 (SAAQRRGR, PGTSGSPI); NS4A (QRTPQDNQL); NS4B (LQAKATREAQKRA) and NS5 proteins (QRGSGQV) in all DENV serotypes. Some serotype specific conserved motifs were also found in NS1, NS5, Capsid, PrM and Envelope proteins. Using comparative genomics and immune informatics approach, we could find conserved epitopes which can be explored as peptide vaccine candidates to combat dengue worldwide.