Background: Betula fujianensis (B. fujianensis), a new Betulaceae species reported in 2008, is endemic and endangered in the Fujian province of China. However, little is known about it, and no special protection measures have been taken. So it is urgent to take some activities for its well conservation.Results: In this study, we systematically described its morphological characteristics, developed a cultivation method, and were the first to report its whole chloroplast genome sequence. We conducted a comparative analysis using its synonymous species (B. luminifera) and identified its distinct characteristic, especially in bark and leaves. It has serrated leaves covered with glandular punctation and short and rare pubescences, and its bark gradually changes with age from smooth to exfoliate. We also observed that its chlorophyll content substantially changes with age. Furthermore, we also sequenced B. luminifera’s chloroplast genome sequence, compared it with that of B. fujianensis, and found that gene rpl16 is absent in B. fujianensis. Phylogenetic analysis also showed that B. fujianensis is relatively close to B. luminifera. Conclusions: These observations and chloroplast genome sequence results provide more information about B. fujianensis. The comparative analysis with B. luminifera will provide some clues to different environmental adaptation. The cultivation method make further scientific researches possible, contribute to its good conservation and promote its utilization in afforestation and industrial application in the future.