Understanding how genomes evolve can help us disentangle the evolutionary history of species, which has practical applications in agriculture. The Camelina genus contains nine species including the emerging oilseed crop, Camelina sativa, and its wild relative, Camelina microcarpa. Hexaploid C. microcarpa is sexually compatible with C. sativa, and diploid C. microcarpa is a potential descendant of one of C. sativa’s progenitors. Thus, these species are likely to have a history of hybridization and polyploidy that is unexplored. We have sequenced and assembled diploid C. microcarpa into 1036 scaffolds covering 73% of the 264Mb estimated genome size, and evaluated its evolutionary relationship with the chromosomes of C. sativa by constructing phylogenies for each conserved ancestral crucifer karyotype (ACK) block. Based on these phylogenies, that C. microcarpa is most closely related to subgenome 2 of C. sativa. Sequencing C. microcarpa is the key step to understand genome evolution in the Camelina genus.