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INTRODUCTION This manual is a general reference for fishery and hatchery managers. Four major topics are covered: 1) the importance of proper management of the genetic resources of fishes, 2) biological principles underlying the genetics of fish, 3) genetic tools and their application to fish populations, and 4) genetic issues in fisheries management. Readers can find answers to specific questions by accessing the appropriate section of the text. A glossary of technical terms and a comprehensive index are also provided. Technical terms found in the glossary are highlighted in the text at their first usage. WHY IS GENETICS IMPORTANT FOR FISHERIES MANAGEMENT? Perpetuation of the resource is the common goal of all fisheries management programs. Genetic factors affect this goal because fish are the product of their genes, the environment, and of the interaction between the two. The genetics of fish, in connection with the environment, determine the quality and persistence of the fishery resource. Fisheries managers must realize that implementation of regulations, stocking strategies, and other management activities affect the genetic make-up of fish stocks. Management activities that impact the genetics of fish stocks include: 1) maintenance of a fishery with adequate natural reproduction, 2) enhancement of a fishery with marginal or inadequate natural reproduction by stocking, 3) rehabilitation of a depleted fishery by stocking or control of harvest, and 4) maintenance of a "put and take" fishery (one with no natural reproduction). Traditionally, managers have concentrated on manipulation of non-genetic, environmental aspects of fisheries (e.g., harvest control, stocking, and pollution abatement). The problem with this approach is that management activities inadvertently affect the genetic make-up of fish stocks. Management costs due to the effects of management activities on the genetics of fish stocks have not been considered. This last point is particularly unfortunate because relatively small and inexpensive changes in management practices may produce substantial improvements in the genetic integrity of a stock. Genetic variation is an important aspect of the genetic makeup of managed fish stocks. The long- term utility of genetic variation is that it enables populations to adapt to changing environments. The genetic diversity in a population is a finite resource that can be used up. Humans can "spend" the genetic diversity in populations to mitigate the impact of their own activities in the short-term. The long-term impact on the perpetuation of the populations is uncertain at best and detrimental at worst. It is important, therefore, to rationally integrate the conservation of genetic variation and the stewardship of fisheries resources. The material covered in this manual lays the foundation for this process. 4