The pea aphid Acyrthosiphon pisum is a worldwide pest that causes serious losses in agricultural production. Drunken horse grass (Achnatherum inebrians) is a widely distributed perennial poisonous grass of grasslands of Northern and Northwestern China. Changes in adult pea aphid transcripts after exposure to aqueous extracts of endophyte-infected (E+) and endophyte-free (E−) plants and distilled water controls (CK) were compared to identify candidate genes and pathways of the pea aphid. The resulting 31,858 unigenes annotations provide useful data for future molecular studies of pea aphid. A total of 147 mRNA transcripts were differentially expressed genes (DEGs): 30 genes were up-regulated and 6 were down-regulated in the E+ versus E− treated aphids; 45 up-regulated and 40 down-regulated genes were identified in E+ versus CK; 23 up-regulated and 3 down-regulated genes were identified in the E− versus CK. KEGG analysis mapped 16, 24 and 42 differentially expressed genes to 13, 20 and 22 substantially enriched pathways for E+ versus CK, E+ versus CK and E− versus CK, respectively. A number of fecundity factors were annotated from 266 unigenes, including fatty acid synthase, aminopeptidase N-like, and cuticular protein genes that were highly expressed in aphids treated with extracts of both E+ and E− plants. Many of these genes were up-regulated at least twofold in E− compared with the E+ treated aphids. The resultant transcriptomic database was authenticated by the transcript levels of five selected fecundity-related genes quantified from different treatment material in a real-time quantitative polymerase chain reaction (PCR). Interestingly, the genes related to lysosome that the most abundant in the E+ and E− treated aphids.Our studies provided the first comprehensive insights into varying treatments and effects on toxicity related genes in aphids. This work will facilitate efforts to explore new biocontrol strategies against pea aphid.