I examine the relationship between reproductive success and marker-based relatedness (MBR; inferred from variation at 21 microsatellite loci) of pair-mates in a semi-isolated population of great reed warblers (Acrocephalus arundinaceus) over a 12 year period. There was a negative relationship between egg-hatching success and MBR, but no association between MBR and three other components of fitness (clutch size, proportion of fledglings and recruits). The relationship between hatchability and MBR was non-linear, with high hatching rates at low and intermediate levels of MBR and a sudden decline in hatching success among the small number of pairs with high MBR (<4% of the sample). It is likely that the decrease in fitness at high MBR was due to effects of homozygosity at genome-wide distributed loci, as opposed to effects of fitness loci in the local chromosomal vicinity of particular markers. This conclusion relies on the fact that similar results were found in another study of the same population that was based on DNA-fingerprinting band-sharing, and that there was a strong correlation between MBR and pedigree-based relatedness. The negative relationship between MBR and hatchability was especially pronounced in the first study years and levelled off in later years. This time-dependent effect of MBR on hatchability was not caused by a simultaneous temporal decrease in MBR, and may instead reflect the importance of other processes such as genotype x environment interactions or purging of deleterious recessive alleles.