Answer: What a fun project! It is difficult to provide a definitive list for a Medieval European flower garden. In those times, most plants were grown for herbal uses. There is very little documentation of what we would consider to be "flower gardens" but here is a list of flowers known to have been in cultivation in Europe by 1600, and most of which are generally thought to have been grown long before then.
Calendula, campanula, European columbine, sweet cicely, chives, hollyhocks and mallows, monkshood, purple foxglove, fleur de lis (Iris pseudacorous), lily of the valley, Madonna lily (Lilium candidum), sweet William, dames' rocket, lilac, mock orange, old world roses such as Apothecary rose and dog rose, liverwort (pulmonaria), Johnny Jump-Up (Viola tricolor) and daffodils.
I would suggest using these in a tiny "door yard" garden: pretty plants tucked in near the kitchen door to be enjoyed by all who pass by. Another alternative would be to use them as part of the herb garden you are already working on. I feel this would be acceptable because many of these plants had herbal uses in addition to being pretty.
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