New Guinea is home to one of the world’s most extraordinary families of birds; the birds-of-paradise (Aves: Paradisaeidae). The family consists of 45 recognised species and many of them have developed remarkable behavioural and plumage traits. Furthermore, the majority of the species reproduce through lek-mating, an extreme form of sexual selection in which female choice determines male mating success. While strong sexual selection is generally considered as a form of pre-zygotic isolation, interestingly, hybrids between distant lineages of birds-of-paradise are well documented across the family. Having fascinated naturalists for centuries, bird-of-paradise specimens have been collected and preserved in natural history collections, including different combinations of putative hybrid specimens. As such, natural history collections represent a remarkable resource for the study of the evolutionary and genomic consequences of interspecific hybridisation in birds-of-paradise. This thesis draws on specimens from natural history collections to study the prevalence of hybridisation and its effect on birds-of-paradise. In chapter I, we present a workflow designed for large scale use of avian museum specimens in genomic studies. The workflow was used to generate genome-wide re-sequencing data for the three other chapters of the thesis. In chapter II, we analyse 37 bird-of-paradise hybrids, originally determined to be hybrids based on morphology. We use genomic methods to verify the hybrid status and the parental species of each hybrid and show that the majority of the specimens are first-generation (F1) hybrids. However, we also identify two specimens that are the result of backcrossing and introgressive hybridisation between different genera. Our findings are the first direct evidence that contemporary introgressive hybridisation takes place between genera of birds-of-paradise in the wild and that interspecific hybrids are not necessarily sterile. In chapter III, we compile a population genomic data set from all seven species belonging to the two genera, Astrapia and Paradigalla. These species inhabit different montane regions across New Guinea but sometimes have overlapping ranges. We find multiple signals of historical gene flow between and within the two genera. Additionally, we present the first empirical genomic evidence of a hybrid zone between two lekking bird-of-paradise species. In the final chapter, chapter IV, we investigate whether introgressed variants may have contributed to the evolution of phenotypic traits in the genera Astrapia, Paradigalla, Epimachus and Drepanornis. We use window-based tests of treeness to pinpoint genomic regions with an excess of shared alleles and further investigate the genes present in these regions and their function. The overarching aim of this thesis was to study to what extent lekking birds-of-paradise still hybridise today, to what degree hybridisation can lead to introgression and whether introgression may facilitate phenotypic evolution.