Abstract: Various biotic and abiotic environmental stresses threaten the productivity of crops. With the development of molecular biology, crop stress research has changed to focus on the regulation mechanisms of stress tolerance at molecular scale, the field today known as ecogenomics. Ecogenomics ecologically integrated the various disciplines of genomic approaches. Here, we reviewed some recent progresses in ecogenomic researches on crop response to biotic and abiotic stresses under the three classes of functional genomics, structural genomics and comparative genomics. Not only the methodologies, but also the applications of genomics in crop stress tolerance were summarized. Specifically, high-throughput approaches based on next generation sequencing were scrutinized. ① Functional genomics, as treated in this review, included transcriptomics, epigenomics, proteomics, interactomics, metabolomics and phenomics. We focused on advances in plant response to stress at gene expression level, which belonged to transcriptomics and epigenomics. A series of vital techniques were introduced, including microarray, RNA-seq, serial analysis of gene expression (SAGE), suppression-substractive hybridization (SSH), bisulfite method, chromatin immunoprecipitation-chip (ChIP-Chip) and ChiP-seq. Recent research results were also discussed, including the functions of transcription factors in crop stress tolerance. It showed that expression of a plant stress factor was regulated by the interaction of the factor with other stress factors of the crop. Several plant stress factors acted in the plant hormone signal transduction pathways. This was more evident for ABA pathway and senescence process as a consequence of stress. It seemed that plants required several transcription factors for the same stress response, whereas the same transcription factor could be involved in different stress responses. Epigenetic studies of epigenetic modifications of genetic materials were about the prevention of change in DNA sequences. Among others, it included DNA methylation, histone post-transcriptional modification and small-RNA-mediated signal transduction. Research also showed that it somehow affected genetic imprint of gene expression. ② Structural genomics was mainly about the utilization of quantitative trait loci mapping (QTL) and DNA sequencing techniques to draw plant genetic maps and genomic physical maps. Due to efficient processes of next generation sequencing, whole genome sequencing was possible for many plants. Until now, whole genome sequencing projects had been completed for only more than forty plants, and more projects were underway. ③ Comparative genetics was based on functional genomics and structural genetics with the aim of investigating the differences and correlations of genomic features among different organisms or populations. It explored the functions of plant stress factors in the evolution process and geographical distribution. Meanwhile, it also provided useful feedback on QTL studies and functional genomic studies. Additionally, various useful online databases on genomic and bioinformatic resources for crop stress research were briefly introduced and some listed. Although some bottlenecks still existed in dealing with numerous genomic data, ecogenomics has already hinted on both basic research on crop stress response and applied strategies for crop improvement.