This paper presents ASDFormer, a novel deep learning-based approach for the diagnosis and biomarker discovery of autism spectrum disorder (ASD). ASD is a complex neurodevelopmental disorder characterized by disruptions in brain connectivity, and functional magnetic resonance imaging (fMRI) offers a noninvasive way to measure this connectivity. ASDFormer captures neural signals associated with autism by incorporating a pooled-classifier expert mixture (MoE) into a Transformer-based architecture that models interactions between regions of interest (ROIs). By integrating multiple expert branches with attention mechanisms, it adaptively highlights brain regions and connectivity patterns associated with autism, enabling improved classification performance and more interpretable identification of disorder-related biomarkers. Implemented on the ABIDE dataset, ASDFormer achieves state-of-the-art diagnostic accuracy and provides powerful insights into functional connectivity disruptions associated with ASD, demonstrating its potential as a biomarker discovery tool.