Traditional genetic manipulation methods have proven ineffective or irrelevant for many citrus breeding objectives. Alternative approaches to Citrus genetic improvement are now available as a result of technological developments in genetics and tissue culture. For example, mapping DNA marker polymorphisms should lead to identifying markers closely linked to important loci, thereby facilitating early selection and minimizing costs associated with plant size and juvenility. Genetic transformation methods allow trait-specific modification of commercial cultivars. By selecting beneficial variants from sectored fruit chimeras and the recovering plants via somatic embryogenesis, the problems of nucellar embryony and the hybrid nature of commercial cultivar groups can be avoided. Induced mutagenesis from mature vegetative buds may overcome these problems, as well as juvenility. Ploidy level manipulation in vitro can increase the number and diversity of tetraploid breeding parents, leading to the development of seedless Citrus triploids and mitigating sterility, incompatibility, and nucellar embryony.