Thalassemia is a single-gene disorder resulting from globin chain synthesis impairment because of the mutation or deletion of globin gene, such as α- and β-thalassemia. Thalassemia occurs with high frequencies in tropical and subtropical regions, primarily in Southeast Asian, Middle Eastern, African and Mediterranean populations. It has been reported that thalassemia is prevalent and variable in southern China, including Guangdong, Guangxi, Guizhou, Yunnan and so on. The spectra of globin gene mutations are diverse and characterized by ethnicity and region in southern China. Analysis of the thalassemia gene mutation types is beneficial to develop the measures to prevention and control the thalassemia. The molecular mechemisms and epidemiology of thalassemia as well as spectra of thalassemia gene mutations in southern China are reviewed.