The genealogical divergence index (gdi) was developed to aid in molecular species delimitation under the multispecies coalescent model, which has been shown to delimit genetic structures but not necessarily species. Although previous studies used meta-analyses to show that gdi can be informative for distinguishing taxonomically good species, the biological and evolutionary implications of divergences showing different gdi values have yet to be studied. I showed that an increase in the calculated gdi value was correlated with later stages of divergence further along a speciation continuum in an Amazonian Hercules beetle system. Specifically, a gdi value of 0.7 or higher was associated with divergences between biological species that can coexist in geographic proximity while maintaining their evolutionary independence. Divergences between allopatric species that could conventionally be treated as subspecific differences, such as geographic taxa that may or may not be morphologically divergent and whose reproductive isolation is likely incomplete, had gdi values that fell within the species delimitation ambiguous zone (0.2 < gdi < 0.7). Although exceptions did exist, different gdi values may prove to be biologically and evolutionarily informative should additional speciation continuums from different empirical systems be investigated, and the results obtained herein can help with objectively delimiting species in the era of integrative taxonomy.