Arthropods are important to worldwide agriculture, food safety, human health, and energy production. Besides their practical significance, various species represent excellent model systems for biological investigations of evolution, development, physiology, reproduction, and social interaction. For these reasons, arthropod genomics is receiving increasing attention from researchers around the globe. Protocols for Cytogenetic Mapping of Arthropod Genomes is a collection of up-to-date, detailed protocols for physical chromosome mapping and their applications for studying genome organization and evolution in insects and ticks. This book brings together the expertise of cytogeneticists working on diverse groups of arthropods. Each chapter demonstrates approaches to tissue dissection, chromosome preparation, fluorescence in situ hybridization, and imaging. The book is a timely and complementary effort to the i5K initiative, which will obtain whole-genome sequences for 5,000 insect and related arthropod species. This comprehensive resource provides cytogeneticists with the necessary background and protocols to understand and develop chromosome-based genome assemblies from such whole-genome sequence data.