Molecular ecology has already provided profound insights into behaviour, ecology and systematics of organisms improving our understanding of the relationship between genetic variation and biodiversity. The objectives of my PhD were to develop new genetic markers and use these markers to address fundamental issues in evolutionary biology using shorebirds as model organisms. Shorebirds are part of the ancient avian Charadriiformes order and are characterised by extraordinary ecological and behavioural diversity. However, due to the lack of appropriate genetic markers the molecular ecology of many shorebirds has not been investigated previously. Therefore, first, I developed polymorphic microsatellite markers from genomic libraries for a behaviourally diverse shorebird, the Kentish plover Charadrius alexandrinus (Chapter II). Second, using the genomic data-bases I expended this work to develop further markers that cannot only be used in the Kentish plover, but also a large number of other shorebird species (Chapter III). Third, I investigated population differentiation and genetic diversity of Eurasian and American Kentish plover populations using the newly developed microsatellite markers and further mitochondrial markers (Chapter IV). The genetic differences between Eurasian and American populations that are mirrored by phenotypic differences call for a reconsideration of the current taxonomic status of the species; Eurasian and American populations should be recognised as belonging to two separate species. Finally, I asked how genetic diversity influences the fitness of precocial Kentish plover young (Chapter V). I found that survival of chicks until fledging was associated with genetic diversity (measured as heterozygosity) at three of eleven marker loci. Genetic diversity at one marker locus had a positive effect on survival whilst it had negative effects at two loci. The results of my PhD have brought up many new questions and I propose promising lines that need to be explored in the future (Chapter VI).