Natural environments impose a multitude of biotic and abiotic challenges to organisms, resulting in both short-term ecological and long-term evolutionary responses. A new interdisciplinary subject, called ecological genomics, integrates ecology, molecular genetics and evolutionary genomics to understand the genetic mechanisms underlying these responses. Ecological genomics introduces the methodology of genomics, such as population genomic, transcriptomic and proteomic techniques, into the study of ecology at individual-, population-, community- and ecosystem-levels. The aim of ecological genomics is to elucidate the genetic mechanisms underlying the responses of organisms to natural environments (including biotic and abiotic environments). This is done by determining which key genes or genetic pathways play important roles in ecological responses and interactions and by exploring the degree of genetic variation in these genes, pathways, and the ecological and evolutionary outcomes. The subjects of ecological genomics are divided into two categories: model species and non-model species. The traditional model species, such as Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis and Caenorhabditis elegans, have well-characterized genetic backgrounds and abundant genetic resources and have played important roles in the development of the field. Non-model systems can serve as important theoretical and practical bases for ecology; attempts to understand variation and molecular mechanisms in natural systems have motivated a shift from laboratory model systems to non-model systems in diverse environments. With the development of genomics methods, an increasing number of non-model species are being studied in ecological genomics. The core techniques used in ecological genomics include methods to detect sequence variation, to measure differential expression of genes, and to link genes to their functions. Novel genomics methods are regularly introduced and applied to the study of ecological genomics. Ecological genomics can be widely applied to ecological questions. It can help to understand the molecular mechanistic basis for responses to abiotic and biotic environments; to explore the genetic and evolutionary bases of species adaptation to abiotic and biotic factors, of phenotypic variation and of ecological speciation; to elucidate the genetic mechanisms underlying how species distribute themselves in space and through geological time, how organisms adapt to global environmental change, and how exotic species become invasive; and to clarify how natural communities are shaped and maintained. Ecological genomics will facilitate the understanding of biotic interactions, evolutionary ecology, global change ecology, invasion ecology, community ecology, and other ecological subfields. Here, we review recent advances in the study of ecological genomics.