Chikungunya (CHIKV) is a positive sense RNA virus of Alphavirus genus in Togaviridae family, transmitted by Aedes albopictus mosquito, commonly known as Asian tiger mosquito. For the mosquito to be infectious, the virus needs to cross two critical barriers, the midgut and the salivary glands. Previous studies have shown that mosquitoes mount an immune response against viral infections. While immune systems of most vertebrate hosts clear infections, mosquitoes remain infected persistently. To identify genes involved in this response, we infected adult female Aedes albopictus mosquitoes with CHIKV by blood-feeding. For the midgut barrier samples, two days post-infection (D2), RNA was extracted from pooled midguts of 6 mosquitoes infected with CHIKV. Control RNA was extracted from 6 pooled midguts of uninfected mosquitoes. For the salivary gland barrier samples, eight days post-infection (D8), RNA was extracted from the heads and the top 1/3rd of the thorax (HT) of 6 mosquitoes infected with CHIKV. Control RNA was extracted from HTs of mosquitoes that were fed uninfected blood. After infectivity status of the samples were verified by RT-qPCR, RNAseq libraries were prepared from three D2 infected samples and two controls, three D8 infected samples and one control using the Nugen Ovation Universal kit v2. The libraries were sequenced on a single lane on an Illumina Hiseq 2500 (2x100 cycles). After quality processing and alignment, using Feature counts and DESeq2 on Galaxy Virtual Lab, differentially expressed genes were identified. Select distinctly immune pathway genes from midgut and salivary gland that were found to be differentially expressed are currently being validated to determine their functional significance during mosquito infection and transmission. The results will help in understanding viral infection of mosquitoes and the information can be utilised to reduce impact of arboviruses by targeting these processes.