We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25X. A total of 1.4 billion 100-bp paired-end (PE) reads was assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 16.7 million single nucleotide variants (SNV) in the three species aligned to the polar bear genome. These data indicate that on average, 0.7% of the nucleotides in the genome are not shared by the three species and polar bears and brown bears share more SNV with each other than either does with black bears. Simultaneous phylogeny and molecular clock estimation from consensus sequences of ultra-conserved elements (UCE) in the nuclear genome resulted in a timetree with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Concatenation and coalescence-based tree reconstructions of approximately one million base pairs of UCE sequence yielded the same topology as the timetree. The divergence time of the black bear lineage and the brown bear/polar bear lineage is estimated at 3.5 million years ago (Ma, range 3.0-3.9), and the divergence of the polar bear lineage and the brown bear lineage is estimated at 1.3 Ma (range 1.0-1.7 Ma) . Genotypes for 162 SNP of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.