Cytogenetic stability is essential for the survival of micropropagated plants. While micropropagation allows rapid propagation of plants with desirable phenotypes, it may also produce genetic variations that are, at times, cytogenetically observable. Factors affecting these variations are not fully understood, and micropropagation protocols are optimized to produce genetically stable regenerants. The genetic stability of micropropagated plants is traditionally assessed by comparing the phenomorphological traits of the regenerants to the mother plant. However, genetic variation does not often result in obvious morphological changes. Therefore, molecular and cytogenetic markers are typically used to evaluate the genetic variations of regenerants. Moreover, analyzing plant genome assemblies is now considered a valuable tool for assessing the genetic stability of micropropagated plants. This review outlines the genetic outcomes of micropropagated plants developed under various culture methods and regeneration pathways and highlights the important roles of genetic markers and techniques in evaluating the genetic stability of the regenerants.