An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with fosmid end-sequence pairs (ESPs) aligned to the human genome reference sequence, we have developed a simple method to resolve human haplotypes using a previously developed clone resource. Partitioning ESPs into either haplotype, we have generated a haplotype-specific clone map for eight diploid genomes (four Yoruba African and four Non-African samples). On average, 59% of each haploid genome is covered by haplotype-assigned clones with an N50 length of 110 kbp. Comparing this clone-based haplotype map against HapMap phased datasets, we estimate an error rate of 0.71% when trio information is available and 6.6% in its absence.