Elephant social structure is matrilineal, with family units composed only of maternally related females and their juvenile offspring, while adult males are mostly solitary and seldom congregate into bachelor herds. In such a social structure, we expect females in the same family unit to have the same mitochondrial genome, which may or may not differ from that of individuals in other family units in the population. Such social structuring also results in the mating males and females having different allele frequencies at nuclear microsatellite loci. This is manifested as an excess of heterozygotes relative to the expected Hardy-Weinberg proportions, a phenomenon which maintains genetic variation within the population by minimizing inbreeding. We analyzed mitochondrial nucleotide sequences and allele frequencies at four microsatellite loci in nine family units of the African elephant (Loxodonta africana) in Queen Elizabeth National Park and found more than one distinct mitochondrial genotype in three of the family units and no significant excess heterozygosity at microsatellite loci in eight of the families. We interpreted these findings as an indication of a breakdown in social structure of this population caused by social stress due to factors like excessive poaching that has taken place in this national park over the last three decades. Ecological and management implications of these findings for elephant populations are discussed.