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ABSTRACT Understanding the structure, functional roles, and assembly of termite communities remains challenging because cryptic diversity, overlapping feeding strategies, and methodological limitations often obscure ecological differentiation. Integrating complementary approaches can address these constraints, yet their joint ability to resolve community structure remains poorly evaluated. Here, we examine how morphological, molecular, stable isotope, and phylogenetic approaches contribute, individually and in combination, to understanding termite community composition, trophic organization, and assembly mechanisms. We applied a standardized integrative framework combining transect‐based sampling, morphological and molecular species identification, stable isotope analyses (δ 15 N and δ 13 C), and phylogenetic community metrics. This framework was assessed using a Caribbean mangrove ecosystem as a case study, where strong environmental filters provide a stringent test of methodological resolution. Six termite species were recorded, reflecting markedly lower richness than is typical of inland tropical forests. Although transect‐based sampling proved effective for capturing species composition, taxonomic completeness alone did not translate into functional or structural differentiation within the community. Stable isotope analyses revealed pronounced trophic overlap and a shared reliance on C 3 plant‐derived carbon, indicating substantial functional redundancy despite taxonomic distinctiveness. Phylogenetic analyses showed no significant clustering or overdispersion, suggesting that community assembly is shaped by stochastic colonization operating within a narrow set of viable functional strategies imposed by environmental filtering. Together, these results show that integrating isotopic and phylogenetic tools with standardized sampling protocols is essential for interpreting the functional meaning of diversity patterns. This combined approach provides a transferable framework for studying community assembly in environmentally constrained and low‐diversity ecosystems.