The first published studies made with a microscope were of honey bees.
Federico Cesi and Francesco Stelluti used their friend Galileo Galilei's new microscope to study the anatomy of the bee and published this work in the broadsheet Apiarium, in 1625. One of the most 'striking aspects' of this document is that they arranged their work in a grid to visually represent their understanding of nature. Five years later, Stelluti published the book Persio, in which he included drawings of honey bees using microscopy.
Article in The Scientist
Digital copy of Apiarium
Digital copy of Persio