The collection of the available range of genetic variation in a gene pool, usually made of the cultivated species and their undomesticated relatives, is referred to as a germplasm collection. Increasingly, discriminator data generated using molecular genetic markers are either complementing or completely replacing those from morphological characters (known as descriptors) in surveys of genetic diversity. In addition to highlighting the state of knowledge on the specific applications of amplified fragment length polymorphisms (AFLPs) in surveys of plant genetic diversity, an attempt at a brief description and comparison of the different marker systems in use has also been made in this chapter. We have also attempted a description of the AFLP marker technology, its strengths and weaknesses, methodologies for generating reliable AFLP data, available resources (hardware, software, consumables); the kinds of questions for which AFLP data provide valid answers; and data management options. This chapter also highlights salient considerations that would guide decisions on the adoption of molecular marker assays.