Chapter 12 Amplified Fragment Length Polymorphism: Applications and Recent Developments Thotten Elampilay Sheeja, Illathidath Payatatti Vijesh Kumar, Ananduchandra Giridhari, Divakaran Minoo, Muliyar Krishna Rajesh, and Kantipudi Nirmal Babu Abstract AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encom- passes in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided. Key words AFLP , cDNA, Epigenetics, Genetic diversity, Transcriptomics, MSAP , Restriction enzymes 1 Introduction The AFLP technique is a patented technology first described by [1] and is applied widely in monitoring inheritance of agronomic traits in plants, pedigree analysis, parentage analysis, screening of DNA markers linked to genetic traits and genes of interest, etc. AFLP technique uses the entire genome for polymorphism and reproduc- ibility and is recognized as a universal DNA fingerprinting system, universally accepted regarding origin and complexity of DNA sam- ples and even small sequence variations that can be identified using a small quantity of DNA as low as 0.05 μg. A large number of Pascale Besse (ed.), Molecular Plant Taxonomy: Methods and Protocols, Methods in Molecular Biology, vol. 2222, https://doi.org/10.1007/978-1-0716-0997-2_12, © Springer Science+Business Media, LLC, part of Springer Nature 2021 187