The in vivo molecular structure of plant mitochondrial DNA (mtDNA) has been a long-standing source of intrigue and controversy. Recent deep sequencing analyses of mitochondrial genomes from numerous plant species have provided the opportunity to revisit this decades-old question from a novel perspective. Whole-genome sequencing approaches have yielded new lines of evidence that the 'master circle' is not the predominant form of plant mtDNA and have revealed striking structural variation both within and among species. Here, I review these recent studies,including the discovery that at least two independent angiosperm lineages have evolved multichromosomal mitochondrial genome structures. These findings raise fascinating questions regarding the mechanisms of plant mtDNA replication and inheritance.