The arrangement of families in the Flora of Nepal follows a modified Englerian sequence. This differs from the precursor publications Enumeration of the Flowering Plants of Nepal and Annotated Checklist of the Flowering Plants of Nepal, which follow Bentham and Hooker's classification. The change to the Englerian system was made to increase comparability between contemporary Floras of Bhutan and China. As in these other Sino-Himalayan Floras monocots will follow the dicots, and genera and species will be treated in taxonomic order , or if there is disagreement over taxonomic order morphologically similar species will be grouped together.
 
The circumscription of families follows the APG IV system, though other arrangements may be followed at the discretion of the Editorial Committee.