Abstract: Homology is one of the fundamental concepts in biology. Recent advances in molecular biology, bioinformatics,developmental biology and evodevotics have led to the wide use of the concept in comparing morphological characters, analyzing molecular sequences, and exploring the molecular basis of the evolution of morphological features. However, because researchers have divergent opinions about the definition of homology, in practice this term is usually used incorrectly, and, thus some false conclusions are drawn. Here, we show how to infer homology and reveal some factors that affect homology. We also point out that the implications of homology should be understood correctly and that homology should be inferred by combining many kinds of evidence to reveal the evolution of genotypes and phenotypes and the relationship between them.