Strong sexual selection due to lek-mating behaviors have evolved extreme and unique sets of morphological ornamentations and behavioral traits in the bird-of-paradise genus Paradisaea(class Aves). Here I use state-of-the-art genomic data to comprehend their genetic divergence, speciation and population structure along with insights into genetic and evolutionary mechanisms of different species of this genus Paradisaea. After careful sample collection a total of 85 Paradisaea samples (acquired from different Natural History Museum collections) were included in the study and evaluated using comprehensive genomic methodologies. The Illuminanext-generation sequencing data were quality assessed and the clean read were mapped against a chromosome level reference genome. Techniques of mitochondrial and nuclear phylogenyanalysis were then employed along with several population genetic analyses to understand the molecular evolution and population structure trends of this genus. mtDNA phylogeny revealedclade where individuals from different species (P. raggiana, P. apoda and P. minor) were mixed indicating gene flow between these recognized species. Nuclear phylogeny, on the other hand, resolved this phylogeny and split these species into distinct groups which were also confirmed by the Principal Component Analyses (PCA). Admixture analysis identified the gene flow between populations of P. raggiana, P. apoda and P. minor. The results are of importance because biogeographical distribution patterns highlight the significance of habitat preservation and genetic diversity maintenance for conservation efforts, since they show both sympatric and allopatric speciation implications. The study advances the knowledge of avian biodiversity and evolution by offering a framework for combining genetic and geographic data in phylogenetic research.