The majority of complete hydatidiform moles (CHMs) harbor duplicated haploid genomes that originate from sperm. This makes CHMs more advantageous than conventional diploid cells for determining haplotypes of single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) as all of the genetic variants in a CHM genome are homozygous. Here we report SNP/CNV haplotype structures determined by analyzing 100 CHMs from Japanese subjects using high-density DNA arrays. The obtained haplotype map should be useful as a reference for the haplotype structure of Asian populations. We resolved common CNV regions (merged CNV segments across the examined samples) into CNV events (clusters of CNV segments) on the basis of mutual overlap and found that the haplotype backgrounds of different CNV events within the same CNV region were predominantly similar, perhaps due to inherent structural instability.