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A Flora describes plants and where they live. Floras typically include a dichotomous key for identification purposes and often times will include range maps as well. Floras are almost always designed to be simultaneously regionally constrained and regionally exhaustive/complete (i.e., includes all plants that grow in that region or at least all taxonomic divisions of specified taxa)
A manual applies much more broadly to plants, and typically instructs you on a subject (e.g., identification/differentiation of species). A manual does not need to be exhaustive and its scope is typically user defined (though often based on the scale/range of it's underlying subject). However, some have used the term manual to be more or less synonymous with Flora or otherwise similar document
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