Amplified consensus genetic markers (ACGM) is a novel PCR-based DNA molecular marker technique, which is based on the conservation of coding sequences and the potential polymorphism within non-coding sequences in homologous genes among closely related species. Along with the rapid development of comparative genomics and bioinformatics, the ACGM technique has already become a powerful tool for comparing homologous genes, analyzing phylogenetic relationships among species, and mapping of genes of interest. Here, an introduction to ACGM technique, especially its application in Brassica genera and Gramineae, was presented in detail. The prospects of ACGM were also discussed.