Apocynum cannabinum is an important economic and ecological crop. Genetic studies on this crop remains largely behind due to the un-availability of genome reference and limited amount of molecular markers. In this study, we performed a whole genome sequencing of?A. cannabinum?by sequencing technology (Illumina), and analyzed the ratios of heterogeneity and repetitive elements, followed by exploration of SSR markers. A total of 31.94 Gb high-quality sequences (Q20 ≥ 90% and Q30 ≥ 85%) have been generated. By searches with NCBI nucleotide database (NT), no exogenous contamination in the sample was detected. De novo assembly and K-mer analysis revealed a genome size of 239.02 Mbp, with 0.56% heterozygosity and 36.72% of repetitive sequences. 273,336 contigs with a N50 of 3,838 bp in length have been detected, and the total length was 222,723,253 bp. 224,587 scaffolds were further assembled, with a N50 of 6,421 bp in length, and the total length was 226,378,236 bp. By predicting for the simple sequence repeats (SSR), 117,511 have been detected potentially for exploring SSR markers. Of all SSR categories, the mononucleotide and hexanucleotide repeat units formed the largest and the least categories, respectively. Thus, this work generated a sequence dataset that might be useful source for future?de novo assembling of?A. cannabinum genome.