Genomic data offers valuable insights into population history and species divergence, but interpreting complex evolutionary processes remains challenging, particularly in cases of recent divergence and ancestral polymorphism. This study addresses the taxonomic and evolutionary complexities of two endemic Hogna spider species from Madeira, H. maderiana from Porto Santo and H. insularum from Madeira, Desertas, Bugio, and Porto Santo, which exhibit mitochondrial gene tree discordance and ambiguous morphological boundaries. Using ddRADseq genomic data, population genomic analyses, and coalescent-based demographic analyses, we aim to determine whether these two nominal species represent a case of early divergence with unsorted molecular markers due to incomplete lineage sorting (ILS), if they are hybridising within the contact zone on the island of Porto Santo, or if they represent a single species exhibiting extreme morphological polymorphism. Our genetic structure analyses suggested three potential genetic clusters, one for each nominal species and one compatible with hybridisation between the two species on Porto Santo Island. However, demographic modelling and D-statistics rejected gene flow, instead supporting the existence of a third independent lineage in Porto Santo. The lack of genetic separation between these lineages likely reflects short recent divergence and unsorted ancestral polymorphisms. Our findings highlight the challenges of inferring hybridisation solely based on population structure analyses, which may lead to an overestimation of gene flow. This study highlights the importance of integrating demographic modelling and genetic data to resolve complex evolutionary histories and emphasizes the need for careful interpretation of genomic data to avoid misattributing gene flow.