alchemical herbals

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JKP,

the description made in the poem refers not to an actual plant, but is a description of the alchemical process itself.
I won't go into full details but basically, this is what the poem says:

First at the Root I will begin, 
That causes all things forth to spring; 
It grows upon a Mountain brim, 
Where Febis [Phoebus] has great domination: 

^this is the Materia Prima


The Root grows on stones clear, 
White and Red, that is so pure: 

^ this is the second matter with which the first is made to react

The Root is black, the Stalk is red; 
It will never be dead, 
The Leaves are round, as a Noble Sun, 
And wax and wane as the Moon: 
In the middle a mark the size of a penny, 
Lo it is like our sweet Lunayre: 
Its Flowers shine, fair and clear, 
[i]In all the World they have no peer,[/i]
^This part refers to the preparation of the Stone: wax & wane= varying intensity of fire to be applied. The mark is the appearance of the beginning of the desired result, announcing the flower= the Stone.

It is not found in no manner wise, 
But by a shepherd in God's service: 
The good shepherd that I here mean, 
Is he who keeps his soul clean: 
^Thîs and the rest of the poem makes explicit that this is not an actual plant but a process to be achieved by a dedicated (and pious!) alchemist.

And thank you, MarcoP, for making this wonderful poem available in modern English.