Cynanchum thesioides, a member of the Asclepiadaceae family, are plants that have been used in traditional Chinese medicine and their latex contains succinic acid which has an important medicinal value. To identify candidate genes involved in succinic acid biosynthesis and accumulation, we analyzed transcriptome data from C. thesioides under drought stress using Illumina sequencing technology. A total of 146 and 172 unique genes were annotated as encoding enzymes involved in the succinic acid biosynthesis of C. thesioides and C. thesioides var. australe and the number of differentially expressed genes (DEGs) was 40 and 32, respectively. As drought stress increased, nine genes were significantly up-regulated and seven genes were significantly down-regulated in C. thesioides. In C. thesioides var. australe seven genes were up-regulated and nine were down-regulated. Enzymes participating in succinic acid biosynthesis were ATP citrate (pro-S)-lyase, succinate dehydrogenase, aconitate hydratase, 2-oxoglutarate dehydrogenase, citrate synthase, glutamate synthase, fumarate hydratase, succinyl-CoA synthetase, succinate-semialdehyde dehydrogenase, glutamate dehydrogenase, isocitrate dehydrogenase, 4-aminobutyrate transaminase, malate dehydrogenase, and glutamate decarboxylase and their activities relating to succinic acid synthesis were determined. RNA-seq sequencing was used in our study. The genes involved in biosynthesis and accumulation of succinic acid in C. thesioides were predicted. Succinic acid content was positively correlated with MDH (BMK_Unigene_033366), but negatively correlated with GAD (BMK_Unigene_096180 and BMK_Unigene_030468), SDH (BMK_Unigene_142841). These results provide an important resource for further research on succinic acid of C. thesioides and other homologous species.