Ricinus communis seeds germinate to a high percentage and faster at 35 °C than at lower temperatures, but with compromised seedling establishment and survival. However, seedlings are able to cope with high temperatures at later stages of seedling establishment if germination occurred at lower temperatures. The identification of this thermo-sensitive window during seed germination suggests that temperature disturb crucial mechanisms that support seedling establishment. We studied the molecular mechanisms that could explain this thermo-sensitive window with a genomics approach using microarray analysis to determine transcriptome changes during seed germination at 20, 25 and 35 °C. Although temperature had a strong effect on the R. communis transcriptome, most of these differences occurred between 6 h of imbibition and the commencement of germination, i.e. radicle protrusion, which coincided with the identified thermo-sensitive window. We identified several responsive genes that might be involved in the thermotolerance of R. communis. Temperature had a major effect on genes involved in energy generating pathways, such as the Calvin-Benson-Bassham cycle, gluconeogenesis, and starch- and triacylglycerol degradation. Transcripts of ATP binding proteins, DNA binding proteins, RNA binding proteins, DNA-directed RNA polymerases, heat shock factor proteins, multiprotein-bridging factor proteins, and zinc finger proteins were also affected by temperature suggesting that transcriptional reprogramming mechanisms were disturbed. Among the downregulated transcripts, three were shared by all three stages: one oxidation-related zinc finger 2, one F-box and wd40 domain protein, and one DNA binding protein/ MYB-like transcription factor. Among the upregulated transcripts, nine were shared by all three stages: one BET1P/SFT1P-like protein 14BB, one low-molecular-weight cysteine-rich protein LCR78, one WD-repeat protein, one GAST1 protein, one adenylate kinase 1/P-loop containing nucleoside triphosphate hydrolases superfamily protein, and four conserved hypothetical proteins. These genes constitute good candidate genes for further characterization of temperature-responsive molecular mechanisms in R. communis, which in turn will provide necessary tools for the exploitation of R. communis by small family farmers under the typical harsh conditions of semiarid regions worldwide.