Molecular cloning is a prerequisite for most molecular applications in soil microbial ecology, regardless of whether the DNA is to be used for community analysis, expression of environmental genes, or metagenomic projects. PCR products are the most common source of material for cloning, and PCR cloning is generally the most straightforward approach. Cloning vectors and kits made specifically for cloning PCR products are widely available, making it a relatively simple process. Cloning of large or low abundance fragments, expression of environmental genes, and screening libraries for specific functions offers significantly greater challenges, however, and potentially greater rewards. A number of strategies for advanced cloning and expression have been developed in recent years, providing great possibilities for analysis and exploitation of functions encoded in soil DNA. Strategies for will be discussed for cloning of PCR products, reverse transcribed mRNA, low abundance transcripts and genes, and construction of phosmid and BAC libraries. Screening libraries for specific functions, such as Substrate Induced Gene Expression Screening, will be briefly discussed.