Mountain systems have long served as hotspots of plant diversification, where complex evolutionary processes can obscure species boundaries and phylogenetic relationships. This dissertation investigated the evolutionary history, polyploidy, and morphological diversification of Rhododendron (Ericaceae) subsection Lapponica and closely related taxa in section Rhododendron, a group that dominates alpine ecosystems in the Himalaya and Hengduan Mountains. By integrating chloroplast phylogenomics, nuclear target-capture sequencing, and quantitative morphological analyses, I examined how geography, ploidy, and morphology relate to species' relationships in this taxonomically challenging group. In Chapter 2, plastome phylogenies from across section Rhododendron revealed frequent discordance with traditional taxonomy. At broad phylogenetic scales, plastid similarity correlated significantly with both geography and ploidy—marking the first reported association between plastome variation and ploidy level in Rhododendron. At finer phylogenetic scales, geographic proximity more often predicted chloroplast similarity than morphological species identity, suggesting geographically structured chloroplast capture via hybridization. Although many species’ relationships within section Rhododendron remained unresolved, a set of diploid taxa formed strongly supported monophyletic clades, offering key reference points for interpreting maternal lineage structure and reproductive isolation. Chapter 3 employed nuclear target-capture sequencing to infer phylogenomic relationships within subsection Lapponica. The clade was resolved as monophyletic, and several diploid species received strong support. However, polyploid taxa frequently clustered by ploidy level rather than by taxonomic species identity, potentially reflecting widespread gene flow, hybridization, and independent origins of polyploid lineages. Cytonuclear discordance was particularly pronounced in polyploid clusters, providing additional evidence for geographic chloroplast capture and reticulate evolutionary histories. Chapter 4 examined whether floral and vegetative morphology corresponded to species boundaries, and similarly, whether clades supported by the nuclear phylogeny in Lapponica aligned with morphological groupings. Morphometric analyses showed substantial overlap in trait values across taxa, with most floral traits offering little taxonomic resolution or phylogenetic signal. Stamen length was the only trait to exhibit consistent and statistically significant phylogenetic conservatism, likely reflecting constraints tied to pollination function. In contrast, floral shape factor traits appeared evolutionarily labile and were not strongly structured by phylogeny. Multilevel linear models showed that ploidy and elevation had minimal influence on floral trait variation. Together, these findings demonstrated that evolutionary patterns in Rhododendron, especially subsection Lapponica, were shaped by a complex interplay of polyploidy, geography, and hybridization, while traditional morphological characters contributed limited resolution for taxonomic or phylogenetic inference. This work uncovered new polyploid information for previously unexamined taxa, clarified some species-level relationships within a dominant alpine shrub lineage, and highlighted the importance of genomic and quantitative approaches in understanding recent and reticulate plant radiations in montane biodiversity hotspots.