The main methods used to estimate population size using capture–recapture for both closed and open populations are described, including the Peterson–Lincoln estimator, the Schabel census, Bailey’s triple catch, the Jolly–Seber stochastic method, and Cormack’s log-linear method. The robust design approach is described. R code listings for commonly used packages are presented. The assumptions common to capture–recapture methods are reviewed, and tests for assumptions such as equal catchability described. The use of programs to select model assumptions are described. The main methods for marking different animal groups are described, together with the use of natural marks and parasites and DNA. Marking methods include paint marks, dyes, tagging, protein marking, DNA, natural marks, tattooing, and mutilation. Methods for handling and release are described.