Zero Trust Architecture (ZTA) principles need rigorous network segmentation and ongoing verification to reduce implicit trust and lateral threat propagation. This paper investigates anomaly detection in software-defined networking (SDN) systems by micro-segmentation, using deep learning models to detect harmful actions that evade traditional coarse-grained monitoring. Two models are developed: a Vision Transformer (ViT) and a 1D Convolutional Neural Network (1D-CNN), which are used to both raw and micro-segmented network flow data. Experimental findings from a simulated zero-trust SDN dataset indicate that micro-segmentation substantially improves detection accuracy. The models trained on segmented input demonstrate enhanced accuracy and F1-scores (F1 = 0.95) compared to those utilizing unsegmented raw data (F1 = 0.90). The ViT-based detector marginally surpasses the 1D-CNN, particularly in recognizing nuanced lateral movement patterns that are unnoticed in unprocessed data. These findings highlight the significance of including micro-segmentation inside zero-trust networks to enhance intrusion detection efficacy. Future efforts will broaden this methodology to include extensive real-world network datasets and dynamic online segmentation techniques.

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