Background: Exploring the biodiversity of any taxon is an important task to disentangle the three of life. Genetics is a powerful tool to uncover biodiversity that eludes visual observation. Identification of cryptic species complexes has experienced a recent increase in the literature due to the inclusion of different types of genetic markers. However, there is still an important research gap in arachnids, where several morphospecies still lack genetic data and few studies explore the effects of biogeographic barriers in shaping their diversity. Spiders are well known to be important ecosystem regulators, yet some genera remain poorly studied. Araneus bogotensis, commonly known as a garden spider, exhibits a broad distribution in the Andes. Current classifications have approached it with caution due to its considerable morphological variation, making it an intriguing subject for investigation. We hypothesized that this species has a complex evolutionary history with multiple cryptic lineages. Methods: To test this hypothesis, we sequenced mitochondrial and nuclear markers, estimated divergence times, ran demographic and species delimitation models and employed a morphometric analysis. Results: Our findings revealed three independent structured lineages that cannot be differentiated by current taxonomic keys. The first lineage comprised most of Colombian populations here sampled, named here as Araneus bogotensis sensu stricto, the second lineage, with an estimated divergence time of 10.9 Mya, comprised individuals from a single population in Serranía del Perijá, North Colombia and the third and oldest lineage comprised a Southern Brazilian population with 18.5 Mya time of divergence. Furthermore, the analyses showed an additional four divergent lineages within A. bogotensis sensu stricto structured by the Magdalena River Valley acting as a strict barrier to gene flow. Conclusions: Our findings revealed cryptic species within what is called Araneus bogotensis, where the geomorphology of the Andes plays an important factor to lineages demography and diversification in Colombia and South America.
