The draft genome of pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next generation sequencing is reported. A 512.0 Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194x coverage. High-density genetic maps comprising of 2,005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. High quality of the assembly and annotation is assessed and confirmed using Sanger-derived BAC sequences along with transcriptome sequences of different tissues. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has re-constructed nine ancestral chromosomes. Pear and apple have diverged from each other ~5.4 to 21.5 MYA, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between apple and pear genomes are confirmed mainly due to presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while, lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3'H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Expansion of S6PDH, SDH, and SOT along with evolutionary relationships of pear and apple have demonstrated their divergence from a common ancestor. Moreover, α-linolenic acid metabolism is a key pathway for aroma in pear fruit.