In situ hybridization is a basic method in modern plant cell and molecular biology. It is used to locate the chromosomal position of genomic DNA sequences. It is able to determine the patterns of gene transcription in mature tissues and during development. In situ hybridization, in combination with other modern methods, has revolutionised our understanding of the structure, function, organization, and evolution of genes and the genome. Here we provide the protocols required for standard RNA and DNA in situ hybridization, with enough background information to enable trouble-shooting and data assessment.