One of the most important breakthroughs in the history of genetics and plant breeding was the development of plant cytology and experimental mutagenesis, which later brought about plant cytogenetics and mutation breeding and now they have entered in functional biology era with the unprecedented development of plant molecular cytogenetics, genetics, and functional genomics. Application of cell biology particularly chromosome biology in the fields of plant genome structure and function has ushered the development of plant cytogenomics. Development of advanced technology like DNA base-specific fluorescence banding, GISH, and FISH-based chromosome painting has greatly facilitated the identification, localization, and mapping of chromosome-specific markers in plants, which is of high importance in plant molecular systematics, species identification, detection of hybrid nature, alien chromosomes and chromosomal aberrations, analysis of somaclonal variations, and diversity analysis. The dynamism of chromatin architecture and cell cycle, representing chromosome functional biology, is another important part of plant cytogenomics. On the other hand, mutagenomics is defined as applied mutation breeding, in which genomic information and tools are utilized in the designing of breeding strategies, screening, selection and verification/authentication of natural and induced mutants, and the utilization of desirable mutations in the breeding processes. Considerable progress has been made in recent times in breeding of cereals, legumes, oil seeds, vegetables, horticultural crops, spices and condiments, fiber-yielding plants, and medicinal and aromatic plants for diverse types of desirable agronomic and functional traits including disease and abiotic stress resistance/tolerance; herbicide resistance; lowering of anti-nutritional factors; enhancement of proteins, minerals, vitamins, essential amino acids, flavonoids, antioxidants, and dietary fibers; enrichment of soil nutrition; enhancement of ornamental, medicinal, and aromatic values; and development of functional and therapeutic foods and other diverse traits related to nutritional quality and high yield. This can be found in a mutant population which carries variant forms of potentially each and every gene present in a particular genome. The functionality of mutagenomics is greatly enhanced due to integration of classical mutagenesis with modern “omics” technology through the development of desirable diploid mutants, recombinant inbred lines, and aneuploid and polyploid lines as effective cytogenetic tools, utilizable in genome mapping and analysis. Functional sets of aneuploid tools are now available in different edible plants, through which several morphological, biochemical, and molecular traits/markers have been assigned on definite chromosomes to construct linkage maps. Recently, induced mutations showing alterations in antioxidant defense response have been identified and tested against diverse types of abiotic stresses to reveal intrinsic cellular and metabolic events toward sensitivity of seed plants to salinity, drought, metal toxicity, and other stresses. These mutations are giving vital inputs, which can be used in formulating effective breeding strategies in different agroclimatic conditions. Mutagenized population has revealed altered pattern of genome response and can also be exploited in enhancing production of natural plant products like antioxidants and flavonoids. Furthermore, these large mutant populations have the potential in reverse genetics approach by employing various techniques, particularly “Targeting Induced Local Lesions in Genomics (TILLING)” technology to better understand gene functions through high-throughput mutation screening, and have been successfully used in major crop plants along with model plant Arabidopsis. The development of mutagenomic approach, thus, provides a cost-effective, clean, and easy-to-use functional tool to increase the genetic diversity and in utilization of this diversity in plant molecular mutation breeding through modern genomic methods. © Springer India 2015.