Bananas and plantains belong to the family Musaceae and are cultivated throughout the humid tropics and sub-tropics. This crop is perennial with a faster relative growth rate compared to other fruit crops, while producing fruit all year round. Because of their nutritional value, bananas and plantains are considered the fourth most important crop worldwide after rice, wheat and corn. In many countries of Africa, bananas are considered an important part of the diet; the population in Uganda consumes per capita an average of 191 kg per year [1]. This crop also represents an important source of income for many rural families that work directly or indirectly in this industry. The edible Musa spp. originate from two wild species, Musa acuminata Colla and M. balbisiana Colla, with the A and B genomes, respectively, as well as their hybrids and polyploids.
The genus Musa is of great importance worldwide due to the commercial and nutritional value of cultivated varieties. Morphological data have suggested that Musa is diverse, with well-defined characteristics giving a number of indicators of the genome constitution. However, phenotyping for many physiological characteristics, including biotic and abiotic stress tolerance, particularly under controlled, contained and reproducible conditions, is difficult because of the size of the plants and their long life cycle.

DNA marker technologies have been widely used in banana genetics and diversity analysis, e.g., in taxonomy, cultivar true-to-type assessment and genetic linkage map development. Currently, proteomic analysis is giving rise to new trends in genetic diversity and plant system biology analyses. These approaches will yield detailed insights into the Musa genome and provide important genetic data for Musa breeders. In this chapter, we discuss the contribution of different DNA and protein-based markers to understanding the genetic diversity of the Musaceae family.