Abstract: Deportation of one set of chromosomes from a strain into the other distinct strain is defined as chromosome substitution. In order to investigate the effects of individual chromosomes they are transferred from a variety to another variety sharing common genetic history. Alternatively, a chromosome carrying a desirable gene or a group of genes may be transferred into another variety lacking those genes. Chromosome substitution in most widely used in plant breeding to developing a resistant variety by advanced mapping populations, including CSSLs, ILs, BILs & NILs. Furthermore, for achieving the objective of enhancing the cultivated species through ingression of novel genes isolated from wild relatives, production of chromosome substitution lines with the help of marker assisted selection acts as the most promising tool. The wild and weedy cultivars of the major crops are sometimes used as germplasm sources in breeding programs. Unwanted effects are more exhibited by alien substitutions rather than alien additions due to which they are not directly used in agriculture.