The recent transition to the online educational domain has increased the need for Automatic Short Answer Grading (ASAG). ASAG automatically evaluates a student’s response against a (given) correct response and thus has been a prevalent semantic matching task. Most existing methods utilize sequential context to compare two sentences and ignore the structural context of the sentence; therefore, these methods may not result in the desired performance. In this paper, we overcome this problem by proposing a Multi-Relational Graph Transformer, MitiGaTe, to prepare token representations considering the structural context. Abstract Meaning Representation (AMR) graph is created by parsing the text response and then segregated into multiple subgraphs, each corresponding to a particular relationship in AMR. A Graph Transformer is used to prepare relation-specific token embeddings within each subgraph, then aggregated to obtain a subgraph representation. Finally, we compare the correct answer and the student response subgraph representations to yield a final score. Experimental results on Mohler’s dataset show that our system outperforms the existing state-of-the-art methods. We have released our implementation https://github.com/kvarun07/asag-gt, as we believe that our model can be useful for many future applications.