Sugar beet (Beta vulgaris subsp. vulgaris) is an economically important crop and provides nearly one third of the global sugar production annually. The beet cyst nematode (BCN), Heterodera schachtii, causes major yield losses in sugar beet worldwide. The most effective and economic approach to control this nematode is growing tolerant or resistant cultivars. To identify candidate genes involved in susceptibility and resistance, the transcriptome of sugar beet and BCN in compatible and incompatible interactions at two time points, was studied using mRNA-seq. In total, 16 cDNA libraries were constructed and 442 691 707raw reads were obtained. In the compatible interaction, many alterations in phytohormone-related genes were detected. The effect of exogenous application of methyl jasmonate and ethephon was therefore investigated and the results revealed significant reduction of J2s infection and female development rates in treated susceptible plants. Our results revealed candidate genes putatively involved in the Hs1pro1-induced resistance, such as genes related to phenylpropanoid pathway, putative R genes and genes encoding F-box proteins, zinc finger and NAC transcription factors, ABC transporters, BURP and CYSTM proteins. Also, the transcriptome of BCN in the infected root samples was analyzed and several nematode effector genes were found. Our study is the first investigation of the transcriptome profile in the compatible and incompatible interactions between sugar beet and BCN. Overall design: Two cultivars of sugar beet, a susceptible and a resistant variety, were infected with Heterodera schachtii. On two time points, 4 days after infection and 10 days after infection, plants were sampled. For each combination of sugar beet type and time point a corresponding non-infected control was sampled as well.