Seeding emergence and tiller number are the most important traits for wheat (Triticum aestivum L.) yield, but the inheritance of seeding emergence and tillering is poorly understood. We conducted a genomewide association study focussing on seeding emergence and tiller number at different growth stages with a panel of 205 elite winter wheat accessions. The population was genotyped with a high-density Illumina iSelect 90K SNPs assay. A total of 31 loci were found to be associated with seeding emergence rate (SER) and tiller number in different growth stages. Loci distributed among 12 chromosomes accounted for 5.35 to 11.33% of the observed phenotypic variation. With this information, 10 stable SNPs were identified for eventual development of cleaved amplified polymorphic sequence markers for SER and tiller number in different growth stages. Additionally, a set of elite alleles were identified, such as Ra_c14761_1348-T, which may increase SER by 13.35%, and Excalibur_c11045_236-A and BobWhite_c8436_391-T, which may increase the rate of available tillering by 14.78 and 8.47%, respectively. These results should provide valuable information for marker-assisted selection and parental selection in wheat breeding programmes.