<p>Natural and anthropogenic disturbances can significantly alter the environmental characteristics of intertidal ecosystem, which in turn can alter the ecosystem structure and impact its species composition. The 2004 Sumatra–Andaman Earthquake-led coastal land uplift (in North Andaman) and subsidence (in South Andaman) had long-term impact on the mangrove ecosystem of Andaman Islands. This study measures the impact of this catastrophic event on the composition of mangrove-associated crab community through functional trait and zeta diversity indices. Representative sites from the uplift (<i>n</i> = 4) and subsided category (<i>n</i> = 4) were compared to quantify species turnover across spatial scales. Additionally, functional trait data (e.g., body size, feeding mode, behavior, etc.) were analyzed to assess the patterns of functional diversity, functional redundancy, functional vulnerability, and trait-mediated persistence under different disturbance regimes. Our results revealed a steeper zeta diversity decline (slope = −&#xa0;7.17) at uplifted sites, indicating higher species turnover and reduced community similarity compared to subsided sites (slope = −&#xa0;6.67). Uplifted sites showed low crab species diversity compared to subsided sites and it was associated with low functional redundancy and high functional vulnerability. Through environmental filtering, traits, such as smaller body size and burrowing behaviors, persisted in uplift sites, while traits, such as omnivory, scavenging, and free-living behavior, persisted in subsided sites. This study highlights the impact of geomorphological changes on the mangrove crab assemblages, revealing its deleterious impact and ecological consequences. Our study provides a robust faunal biodiversity assessment framework for dynamic coastal ecosystems such as mangroves.</p>