Biodiversity is an important material basis for human survival. China has done a lot of work in the field of biodiversity and published many valuable papers. With the bibliometric method, this study made statistics on the number and citation of papers included in the Web of Science (WOS) and in the China National Knowledge Internet (CNKI ) database of biodiversity research in China from 2009 to 2018. Additionally, the author cooperation, cooperative institutions, national (regional) cooperation and research hotspots of the papers were analyzed using CiteSpace. The results showed that there were 17035 papers in the field of biodiversity research in China from 2009 to 2018, including 13365 CNKI papers and 3670 WOS papers. Both the annual total number of papers and the annual number of WOS papers showed overall upward trends. The title of the most frequently cited CNKI papers was ‘Methods and protocols of plant community inventory’, which published in the journal Biodiversity Science in 2009. And, the title of the most frequently cited WOS papers was ‘TRY - a global database of plant traits’, which published in the journal Global Change Biology in 2011. Professor Piao Shilong, Professor Luo Yiqi and Professor Tang Zhiyao were the core authors in the biodiversity research field based on the WOS literatures. Professor Wang Dexiang, Professor Ma Keping and Professor Zhang Wenhui were the primary authors in the biodiversity research field based on the CNKI literatures. The institutions with the largest quantities of WOS papers and CNKI papers were all the research institutions from the Chinese Academy of Sciences. There were 106 countries or regions that cooperate with China, including the United States, the United Kingdom, and Australia. The journal analysis showed that Acta Ecologica Sinica and Global Change Biology were the primary journal carriers of Chinese and foreign papers in this field, respectively. There were two research hotspots based on WOS papers, one was the effects of environmental factors such as the climate and soil on species diversity, and the other was the analysis of genetic diversity of species using microsatellite molecular marker technology. The research hotspots based on CNKI papers were the relationships between environmental factors and community structure. The present study quantitatively and objectively investigated the status and hotspots of biodiversity research in China from 2009 to 2018, which could promote in-depth in this field and provide reference information for scholars in the relevant fields to refine their research directions and allow them to address specific scientific issues.