Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.