Widely distributed (WD) species are known to exhibit phenotypic variations across their distributional range. However, there is no consensus regarding the underlying factors that contribute to this variation. Here we explore whether factors such as geological events, dispersal constraints, and hybridization events govern the genetic diversity within a WD species. We studied the widespread ginger lily Hedychium spicatum, found in the understory of the Asian tropical montane forests and is morphologically variable across its geographical range. Using single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) we investigated the genetic structure of H. spicatum using model-based and model-free approaches. Our results show that H. spicatum is shaped by historical factors such as i) demographic fluctuations due to glaciation in the Himalayas, ii) dispersal constraints, and more recent factors such as iii) ploidy variations, and iv) hybridization events. We identified intermediates, hybrid species, and cryptic species across its distributional range, which are a result of multiple instances of gene flow between the widely distributed H. spicatum and at least four co-occurring, congeneric hedychiums. We show that the Western Ghats population is an example of long-distance migration from the Himalayas, which is undergoing progenitor-derivative speciation, confusing taxonomists to wrongly identify H. venustum as a new species, rather than an admixed variant of H. spicatum. In summary, the morphological, genetic, and taxonomic complexities within H. spicatum highlights the emergent-system-like characteristics in this WD species, and that WD species provide a glimpse of speciation on a spatial scale.