Riparian ecosystems are disproportionately biodiverse and vital to many taxa despite their scant footprint on the landscape. Yet globally they are also under the greatest human-caused threats. The loss of habitat is the greatest driver of species declines, but fragmentation may also significantly impact populations by creating barriers to dispersal. Effective conservation requires an informed understanding of species' threats and capabilities, though it is unclear whether the increasing fragmentation of riparian woodland in western North America is affecting dispersal patterns of riparian breeding birds. Research suggests long distance migrants may be less impacted than resident species, though previous genetic research on the threatened western population of the yellow-billed cuckoo (Coccyzus americanus), a long-distance Neotropical migrant and obligate riparian breeding bird, suggests local structuring among isolated western populations. There is also interest in using more informative markers to assess genetic differentiation between eastern and western yellow-billed cuckoos. Despite limited differentiation found in mitochondrial sequences between eastern and western cuckoos, analysis of microsatellite markers is expected to reveal significant population structuring. Comparing 14 polymorphic microsatellite loci among seven separate populations in the west, and between western and eastern samples, I found limited population structuring, suggesting sufficient dispersal is occurring to maintain gene flow, both among isolated western, and between western and eastern populations. I found lower than expected heterozygosity across the range, possibly due in part to higher rates of inbreeding experienced by small populations, though the results were clouded by a high number of estimated null alleles downward-biasing estimates of heterozygosity. To test the accuracy of the microsatellites and measure scoring error, I compared microsatellites and mitochondrial sequences in nesting groups sampled from high-density restoration sites on the lower Colorado River. To identify the nesting males and females, I modified a universal avian sexing protocol, optimizing it for yellow-billed cuckoos. I calculated a scoring error rate of 2.12%, 0.91% not explained by null alleles. I also confirmed a relatively high rate of conspecific nest parasitism, with the nesting male apparently fathering the parasitic young in many cases. This is the first assessment of the relationships among breeding adults and nestlings of this species. With more nests providing more egg-dumping opportunities, the productivity of parasitic females should increase with larger populations of nesting cuckoos. Restoring more large patches of functional riparian woodland, to support multiple nesting pairs, could help to recover this declining population.