Although there were many ancient Chinese mathematicians contributed a lot on geometry, Geometric morphometrics (GM) in modern concept was not firstly proposed by Chinese. The super capability of geometric morphometrics in scientific computing and problem solving has gained a lot of attentions in the world. Until early of 21 centuries, geometric morphometrics was introduced into China. Since then, GM was rapidly applied in many research fields. However, it is a pity that GM is still not well-known in China as many works are published out of China. Thus, the special issue "Geometric morphometrics: Current shape and future directions" is organized. The present issue presents a series of contributions in this scientific field. In future, there will be many considerable new developing fields on GM needed to pay more attentions, for instances, 3D geometric morphometrics, 4D analysis, visualization of amber, new machine developing, new software developing, automatic identification system, etc. Once these technical bottle-necks on 3D data collecting and merging geometric morphometric data from multiple characters could be solved, the automatic identification system and other fields based on Big Data would come true.