Phylogenomics has transformed insect systematics by expanding the number and genomic distribution of characters available for species delimitation, yet greater data volume does not remove the assumptions that connect sampled organisms to taxonomic conclusions. This methodological review examines that inferential chain across sampling design, locus and genome representation, species-tree models, gene flow, delimitation algorithms, threshold and prior sensitivity, and reproducibility. The central problem is that different analytical layers answer different questions: a mitochondrial partition, genomic cluster, gene tree, multispecies-coalescent result, or morphometric discontinuity is evidence about biological structure, but none is automatically identical to a species boundary. Insect case studies further show that discordance may reflect sex-biased dispersal, hybridization, ancestral introgression, rapid lineage splitting, inadequate taxon sampling, technical contamination, or method-specific partition behaviour. The review therefore treats discordance as information to diagnose rather than noise to suppress. It develops a proposed assumption-to-conclusion architecture in which evidence is carried forward with explicit representation, model, sensitivity, and validation boundaries. The intended outcome is not a universal delimitation rule, but a more reproducible way to state what a species hypothesis is supported by, what assumptions it inherits, where competing interpretations remain plausible, and what additional evidence would discriminate among them.
