Aedes (Stegomyia) aegypti, the principal global vector of dengue viruses, has differences in its susceptibility to dengue virus infection. We compared the global expression of genes in the midguts of Colombian Ae. aegypti dengue‐susceptible (Cali‐S) and dengue‐refractory (Cali‐MIB) field derived strains after ingesting either a sugarmeal, a bloodmeal, or a bloodmeal containing dengue virus serotype 2 (DENV‐2). Microarray‐based transcriptome analysis among treatments indicated a total of 4725 transcripts with differential expression between the two strains. Eleven genes were selected from different functional groups based on their significant up or down expression levels as well as reports in the literature suggesting they are associated with dengue virus elimination. We measured mRNA abundance of these 11 genes at 0, 8, 24, and 36 h postinfection using quantitative real time PCR (qPCR) to confirm the microarray results and assess any temporal patterns. Four genes were selected (Gram‐negative binding protein—GNBP [AAEL009176], Niemann Pick Type‐C2—NPC2 [AAEL015136], Keratinocyte lectin [AAEL009842], and Cathepsin‐b [AAEL007585]) for knockdown experiments using RNA interference (RNAi) methodology to determine the phenotype (DENV‐2 susceptible or refractory). Silencing GNBP, Cathepsin‐b and Keratinocyte lectin reduced the percentage of mosquitoes with disseminated virus in the Cali‐S strain to 8%, 20%, and 12% respectively compared with 96% in the controls. Silencing of NPC2 increased the percentage of mosquitos with disseminated virus infections in Cali‐MIB to 66% compared with 35% in the controls. This study provides insight into genes that may contribute to the Cali‐S susceptible and Cali‐MIB refractory phenotypes in Ae. aegypti.