Members of the Botryosphaeriaceae are known to be cosmopolitan and occupy crucial niches in ecosystems. Some species are economically important pathogens, causing serious die-back, cankers, and leaf spot diseases of woody plants. The others are saprobes, endophytes or as potential pathogens in agriculture and forestry. They have large numbers of species and a broad host range. The up-to-date advances in molecular ecology of the Botryosphaeriaceae were reviewed. Firstly, a brief introduction to the developmental history on the species identification and the methods was made. Six new genera and 38 new species published after 2006 were listed, six new species of which were from China belonging to the genus Guignardia. At the same time, a large number of species were treated as synonymys, but some synonyms, e.g. Botryosphaeria berengeriana were still used in some countries such as China and Japan. Phylogenetic relationships among these genera and species were discussed and 18 groups were recognized within this family based on morphology and DNA sequence data, including large subunit (LSU) and the internal transcribed spacer (ITS) regions 1 and 2 and the 5.8S gene of the ribosomal RNA, the portion of gene encoding translation elongation factor 1 alfa (EF1-α) and Bt2 regions of the beta tubulin gene (β-tubulin). Moreover, the genus Dothidotthia, which formerly was treated as a member of the Botryosphaeriaceae, was eliminated. In the respect of population genetic structure and patterns of host association, botryosphaeriaceous fungi were divided into two groups, host specialization and host neutralization. In general, members in Botryosphaeriaceae did not show an obvious host specialization, while some populations displayed a certain degree of host association. The associations between Botryosphaeria spp. and their host plants were revealed, which showed that Diplodia pinea and D. scrobiculata only occur on Pinus and other conifers, Neofusicoccum eucalyptorum and N. eucalypticola only occur on Eucalyptus, and N. protearum and Saccharata protea only occur on Proteaceae. Intra-specific genetic diversity and gene flow in Botryosphaeriaceae were successfully investigated using inter-simple sequence repeat (ISSR), simple sequence repeats (SSR), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and other molecular marker methods. The level of genotypic diversity of Diplodia pinea populations were compared using SSR method. It is South Africa, New Zealand, and Australia from high to low in turn and the morphotype B of D. pinea were most diverse among all the four morphotypes. Lasiodiplodia theobromae populations from different host plants and regions were analyzed using SSR method. The results indicated that they are not host-specialized and gene flow is very strong among different hosts but limited geographic regions. It is of certain directive significance to control diseases caused by Botryosphaeria spp. to review status of molecular ecology of these fungi. Finally, deficiency of present researches was pointed and problems need to be solved in future research were briefly proposed.