Coastal cities exert intense anthropogenic pressure on marine ecosystems, reshaping biodiversity patterns and creating novel ecological outcomes. Yet, urban marine biodiversity remains poorly understood and underrepresented in research. Across comparative studies and projects conducted in two subtropical coastal megacities/regions, we combined standardized benthic samplers with molecular tools to investigate how urbanization shapes biodiversity at multiple spatial-temporal scales and organismal groups. First, ARMS-based (Autonomous Reef Monitoring Structures) surveys conducted along urban pollution gradients revealed that richness was highest at an intermediately disturbed site but did not differ significantly among sites. However, community composition varied greatly, with only a small fraction of taxa shared across sites, revealing a fine-scale spatial mosaic where each location supported a largely distinct assemblage. Second, fouling community transplantation experiments showed that historical contingency and assembly history strongly shape succession trajectories, regardless of strengths and types of urban stressors. Third, while microbial communities in urban estuaries and lagoons were structured primarily by salinity and seasonality, urban runoff markedly altered their distributions, with antimicrobial resistance genes concentrated near locations with high levels of human activities and settlements. These findings argue against the binary classification of habitats as either "pristine" or "degraded", highlighting the need for new paradigms for evaluating urban marine biodiversity. Transitional and moderately impacted sites can harbor locally unique biodiversity that simple management frameworks risk overlooking, and the most impacted sites can still support diverse communities not found elsewhere. Together, we advocate holistic, evidence-based planning that embraces the spatial heterogeneity of urbanized seascapes. With thoughtful management, even highly urbanized coastlines can support diverse, resilient, and functionally important marine communities.