Objectives: Dental caries is a highly prevalent chronic condition that, if left untreated, can result in severe oral health consequences, including pain, infection and tooth loss. Micro-invasive treatments for dental caries, such as fissure sealants, are effective in arresting incipient caries in pits and fissures. However, conventional sealants face challenges such as technique sensitivity and failure under moisture contamination. Hydrophilic sealants were introduced to address these limitations, offering better adaptability in moist environments. Marginal sealing is a critical factor in determining the longevity and success of restorative treatments. Methods: The study utilized 20 extracted sound molar teeth free from caries and developmental defects. The samples were randomly divided into two groups of 10 each: Group I (Ultra-seal XT Hydro hydrophilic sealants) and Group II (Flowable composite). Mesiodistal sectioning was performed using a low-speed diamond cutting blade and the sections were immersed in 0.1% rhodamine B isothiocyanate dye at 37°C for 24 hours. Dye penetration was assessed using confocal laser scanning microscopy. Microleakage was evaluated following Ovrebo and Raadal guidelines (1990). Results: Group I (hydrophilic sealants) exhibited significantly less dye penetration compared to Group II (flowable composites), as determined by the Mann-Whitney U test (p = 0.041). The results indicated that hydrophilic sealants demonstrated superior marginal sealing, reducing microleakage more effectively than flowable composites. Conclusion: Hydrophilic sealants showed better performance in preventing microleakage than flowable composites, particularly in moisture-prone conditions. These findings suggest that hydrophilic sealants are a valuable choice for enhancing the longevity and effectiveness of restorative treatments, with potential implications for improving clinical protocols and patient outcomes. Future research should explore the long-term durability, cost-effectiveness and real-world applications of these materials.