Maize (Zea mays L.) is one of the cereal crops broadly adapted worldwide. Enhancement of maize production and productivity can be achieved through identification of potentially superior inbred line combinations in the form of hybrids. The objective of this paper is to understand the relationship of hybrids performance and AFLP based genetic distance and review the molecular basis for heterosis. Morphological markers have shortcomings to detect differences among closely related genotypes and influenced by prevailing environmental conditions. Molecular markers are not influenced by environmental factors and also fast, efficient and more sensitive than field testing to detect large numbers of distinct differences among genotypes at the DNA level. In maize, AFLP techniques have been applied to genome mapping, DNA fingerprinting, genetic diversity studies and hybrid performance prediction. Genetic markers represent genetic differences between individual organisms or species. There are three major types of genetic markers: (1) morphological markers which themselves are phenotypic traits or characters; (2) biochemical markers, which include allelic variants of enzymes called isozymes; and (3) DNA (or molecular) markers, which reveal sites of variation in DNA. Prediction of hybrid performance is one of the main goals in almost all maize hybrid breeding programmes. Information on germplasm diversity and relationships among elite materials is of great importance in maize hybrid development. Genetic distance has been used to predict hybrid performance and the efficiency of prediction was greater with cross between inbred lines from the same heterotic group then cross between inbred lines from different heterotic groups.