Tobacco (Nicotiana tabacum L.), a model organism for research, is also an economically important crop. Tobacco is an allotetraploid derived from interspecific hybridization involving the two diploid species Nicotiana sylvestris and Nicotiana tomentosiformis. Nicotiana tabacum’s genome is complex and its functional genes are often duplicated with multiple homologs. Recently, various organizations have presented draft genomes for three major tobacco types. Here we report a high coverage genome for Burley tobacco and genomic comparisons among Burley, flue-cured, dark, Maryland and Oriental tobaccos. These studies reveal that genetic relationships between these different tobaccos are closely linked but they also have unique genetic identities corresponding to their representative properties. We have also developed a whole genome Axiom^® SNP chip and have generated SNP profiles for over 30 additional tobacco lines that serve as important base breeding material. These efforts have provided for rapid recovery of novel traits as well as introgression of traits of interest into elite germplasm. Genes and their functions also provide the basis for understanding tobacco complexity which leads to novel trait discovery including low constituent tobacco with superior leaf quality. Genome based gene functional analysis will lead to a thorough understanding of the impact that tobacco genes have on agronomic performance and quality traits as well as provide a better understanding of tobacco as a crop, and not just a model organism.