Objective Deinococcus radiodurans (D. radiodurans) is an extremophile with strong resistance to ultraviolet (UV), ionization, desiccation and chemical reagents. However, the molecular responses of this bacterium in the early recovery stage after UV irradiation are not fully understood. The aim of this work is to reveal the transcriptomic responses of D. radiodurans at this stage.Methods In this study, the transcriptomes of D. radiodurans under normal and UV irradiation culture conditions were determined by using RNA-seq technique. To identify the key genes and their regulatory relationships among the differentially expressed genes (DEGs), functional enrichment analysis was performed. Some key DEGs were selected and validated by real-time quantitative PCR. The transcriptome data from previous studies were adopted to find DEGs common to UV irradiation, ionizing radiation and desiccation stresses. The protein-protein interaction (PPI) network of DEGs was constructed; the hub genes and major modules in the PPI network were identified; functional enrichment analysis was performed for these hubs and modules.Results The results showed that the number of up-regulated genes was more than twice that of down-regulated genes in the early recovery stage after UV irradiation, and most of them were related to stress response and DNA repair. The main repair pathways in the early stage of recovery include single-strand annealing (SSA) pathway (involving genes ddrA-D), nonhomologous end joining (NHEJ) pathway (involving genes ligB and pprA) and nucleotide excision repair (NER) pathway (involving genes uvrA-C), the first two of which are for homologous recombination (HR), while the NER pathway removes pyrimidine dimers caused by UV irradiation. By comparing the transcriptome data under UV irradiation, ionizing radiation and desiccation stresses, it was found that the common responsive DEGs mainly involve Deinococcus-specific genes and the genes related to DNA/RNA metabolism. Several important hub genes and interaction modules were identified from the PPI network of DEGs, whose functions are concentrated in double-strand break repair, DNA topological change and replication.Conclusion These results indicate that in the early recovery stage after UV irradiation, a variety of genes in D. radiodurans undergo responses at transcriptome level, several repair pathways are initiated to cope with this stress, and some repair pathways are common to other stress conditions.