Silicon (Si) uptake and accumulation in plants can mitigate various biotic stresses through enhanced plant resistance against wide range of herbivores. But the role of silicon in defense molecular mechanism still remains to be elucidated in finger millet. In the present study, we identified three silicon transporter genes viz. EcLsi1, EcLsi2, and EcLsi6 involved in silicon uptake mechanism. In addition, the study also identified and characterized ten different Si transporters genes from finger millet through transcriptome assembly. The phylogenetic study revealed that EcLsi1 and EcLsi6 are homologs while EcLsi2 and EcLsi3 form another pair of homologs. EcLsi1 and EcLsi6 belong to family of NIP2s (Nod26-like major intrinsic protein), bona fide silicon transporters, whereas EcLsi2 and EcLsi3, an efflux Si transporter, belong to an uncharacterized anion transporter family having a significant identity with putative arsB transporter proteins. Further, the phylogenetic and topology analysis suggest that EcLsi1 and EcLsi2 co-evolved during evolution while, EcLsi2 and EcLsi3 are evolved from either EcLsi1 and/or EcLsi6 by fusion or duplication event. Moreover, these silicon transporters are predicted to be localized in plasma membrane, but their structural differences indicate that they might have differences in their silicon uptake ability. Silicon amendment induces the synergistic defense mechanism by significantly increasing the transcript level of silicon transporter genes (EcLsi1, EcLsi2 and EcLsi6) as well as defense hormone regulating genes (EcSAM, EcPAL and EcLOX) at 72 hpi (hours of post infestation) in both stem and roots compared to non-silicon treated plants against pink stem borer in finger millet plants. This study will help to understand the molecular defense mechanism for developing strategies for insect pest management.