Abstract: Dealing with the missing values is an important object in the field of data mining. Besides, the properties of compositional data lead to that traditional imputation methods may get undesirable result if they are directly used in this type of data. As a result, the management of missing values in compositional data is of great significant. To solve this problem, this paper uses the relationship between compositional data and Euclidean data, and proposes a new method based on Random Forest for missing values in compositional data. This method has been implemented and evaluated using both simulated and real-world databases, then the experimental results reveal that the new imputation method can be widely used in various types of data sets and has good performance than other methods.