Many practical applications require synthesizing directed graphs that satisfy the acyclic constraint along with some side constraints. Several methods have been devised for encoding acyclicity of directed graphs into SAT, each of which is based on a cycle-detecting algorithm. The leaf-elimination encoding (LEE) repeatedly eliminates leaves from the graph, and judges the graph to be acyclic if the graph becomes empty at a certain time. The vertex-elimination encoding (VEE) exploits the property that the cyclicity of the resulting graph produced by the vertex-elimination operation entails the cyclicity of the original graph. While VEE is significantly smaller than the transitive-closure encoding for sparse graphs, it generates prohibitively large encodings for large dense graphs. This paper reports on a comparison study of four SAT encodings for acyclicity of directed graphs, namely, LEE using unary encoding for time variables (LEE-u), LEE using binary encoding for time variables (LEE-b), VEE, and a hybrid encoding which combines LEE-b and VEE. The results show that the hybrid encoding significantly outperforms the others.