Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process of parasitism, RNAs from different stages, i.e. seed, seedling, vegetative strand, prehaustoria, haustoria, and flowers, were used to de-novo assemble and annotate the transcriptome of the obligate plant stem parasite Cuscuta pentagona (dodder). The assembled transcriptome was used to dissect transcriptional dynamics during dodder development and parasitism, and identified key gene categories involved in the process of plant parasitism. Host plant infection is accompanied with increased expression of parasite genes underlying transport and transporter categories, response to stress and stimuli, as well as genes encoding enzymes involved in cell wall modifications. By contrast expression of photosynthetic genes is decreased in the dodder infective stages compared to normal stem. In addition, genes relating to biosynthesis, transport and response of phytohormones, such as auxin, gibberellins and strigolactone, were differentially expressed in the dodder infective stages compared to stem and seedlings. This analysis sheds light on the transcriptional changes that accompany plant parasitism and will aid in identifying potential gene targets for use in controlling infestation of crops by parasitic weeds.