Western gorillas Gorilla gorilla have been exceedingly difficult to habituate to the presence of human observers. Nevertheless, researchers have amassed a wealth of information on population densities and group structure for this ape species by locating and counting the sleeping nests of wild individuals. Such nest-count studies have suggested that western gorilla groups often have multiple silverbacks and these multimale groups occasionally divide into smaller subgroups. However, observational data from forest clearing sites and from a few recently habituated western gorilla groups show no evidence of multimale family groups or of subgrouping. This discrepancy underscores a long-standing question in ape research: How accurately do nesting sites reflect true group compositions? We evaluated these indirect measures of group composition by using DNA from faeces and hair to genetically identify individual gorillas at nesting sites. Samples were collected from unhabituated wild western gorillas ranging near Mondika Research Center in the Central African Republic and Republic of Congo. DNA extracted from these samples was genotyped at up to 10 microsatellite loci and one X–Y homologous locus for sex identification. Individuals were then identified at nesting sites by their unique multilocus genotypes, thus providing a ‘molecular census’ of individual gorillas. Results confirm that western gorillas often build more than one nest at a nesting site and, thus, nest counts can be highly inaccurate indicators of group size and composition. Indeed, we found that nest counts can overestimate group size by as much as 40%, indicating that true gorilla population numbers are probably lower than those reported from census surveys. This study demonstrates how genetic analysis can be a valuable tool for studying and conserving elusive, endangered animals.