The development of gene-mapping methodology has not been a linear process. Instead, this development has been multidimensional, culminating in the creation of a powerful and heterogeneous collection of tools. A description of the history of the development of this would include words such as “opportunistic” (i.e., capitalizing on the newest developments in computer technology and genomics) and “problem-solving oriented” (i.e., constantly addressing issues (such as the spotted nature of linkage disequilibrium) that arose during the development of the methodology). Therefore, the following presentation is method-oriented rather than problemoriented. In describing the modern methodology of gene mapping, attempts will be made to describe the origin of a given methodology, the problems it was designed to address, and its known strengths and weaknesses.