Bayer CropScience management board member Dr Rüdiger Scheitza said:
"This acquisition not only further strengthens our successful fruits and vegetables business - Prophyta´s patented solid-state fermentation technology and strong expertise in the formulation of live fungal spores will also help us bringing new, innovative solutions to market."
Among Prophyta's product range are Contans for control of Sclerotinia, and the nematicide BioAct.
It has around 30 full-time employees.
The move follows Bayer's acquisition last summer of US biological control specialist firm AgraQuest.
Bayer will begin selling AgraQuest's biological fungicide Serenade under its own branding this coming season.