Nalaila, S. M., Stothard, P., Moore, S. S., Wang, Z. and Li, C. 2011. Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle. Can. J. Anim. Sci. 91: 61-73. Quantitative trait loci (QTL) mapped to large chromosomal regions have limited utility as DNA markers for marker-assisted selection (MAS) and are less informative as a reference for the identification of the underlying causative quantitative trait nucleotides (QTN). The objective of this study was to conduct a whole genome fine mapping of QTL for ultrasound and carcass merit traits in beef cattle using a greater density of single nucleotide polymorphism (SNP) markers, and to identify SNP markers within the QTL regions that are associated with the traits. A total of 418 steers from 28 sires were used in this study with nine ultrasound and seven carcass merit traits that were collected as part of a feedlot trial conducted from 2003 to 2005 at the University of Alberta Kinsella ranch. Sires and their progeny were genotyped for a total of 4592 SNP markers distributed across all 29 bovine autosomes (BTA). Across-family analyses detected 12 QTL for five ultrasound traits on nine chromosomes and 18 QTL for six carcass merit traits on 10 chromosomes (P<0.05). Within-family analyses identified 78 significant QTL for nine ultrasound and seven carcass merit traits (P<0.01). The use of a denser panel of SNP markers allowed fine mapping of QTL to smaller chromosomal regions ranging from 0.6 to 11 cM compared with relatively larger QTL regions of 4 to 24 cM reported in previous studies. Furthermore, single SNP marker association analyses identified 22 SNPs that were significantly associated with three ultrasound and four carcass merit traits under 12 QTL regions (P<0.05). These identified SNP markers significantly associated with the traits under the fine mapped QTL regions provide genomic tools for potential application of MAS and a reference to assist with the identification of QTN causing variations in ultrasound and carcass merit traits in beef cattle.