MCScanX is a tool for detecting and analyzing intraspecific and interspecific genomic synteny as well as gene duplication events. Based on the chromosomal positional information of genes, it identifies collinear blocks within genomes, and further infers chromosomal homology relationships among species and the evolutionary history of genomes accordingly. MCScanX can distinguish various types of gene duplication events, such as whole-genome duplication, tandem duplication and segmental duplication. It serves as a vital tool for research on plant genome evolution and comparative genomics.