Stoichiogenomics is a newly arisen research field, which concerns the element usage biases of biological macromolecules at genome, transcriptome, proteome, metabonome levels. Different biological macromolecules have different element compositions and contents. When the supply of some elements was constrained, natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules. This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies, more and more available metagenomic and metatranscriptomic data, and the applications of new analysis strategies. As a newly emerged cross discipline field, stoichiogenomics integrates stoichiometry, ecology, evolutionary biology, genomics and bioinformatics to provide a whole new perspective for investigating the interactions of the macromolecular evolution and ecosystem, and data mining in the post genomic era. In this review, we summarize the latest research progress of stoichiogenomics from the aspect of the element usage biases in proteins and nucleic acids. Furthermore, new research directions are discussed to provide some valuable references for the research and application of stoichiogenomics.