Documents giving evidence of plant collection and teaching activity evolution in the Botanic garden of Padua during the centuries, are discussed. The manuscript “Semina Horti Medici 1614” by the Prefect Prospero Alpini, is regarded as the first “Index Seminum” of the Garden. The manuscript by Giulio Pontedera (Prefect from 1719 to 1757) provides the lists of plants cultivated by his predecessors and suggests several synonyms, therefore making easier the botanical identifications of plants indicated with pre-linnean polynomial names. A bound volume containing 950 dried specimens of plants from the Botanic Garden of Padua, still exists at the Museo della Farmacia in Bressanone (Italy). This herbarium, dated 1653, assembled by a gardener, purchased by the medicine student Angermann from Innsbruck who wrote the latin plant names, is particularly valuable in confirming the identity of the plants listed in 1644 and 1660 by the Prefects Wesling and Dalla Torre; moreover, it provides evidence of a new method of teaching. The manuscript written at Bysantium in 1734 by the physician Alessandro Knips Macoppe jr., contains the full text of the lessons of “Ostensio simplicium” held by the Prefect Giulio Pontedra, who illustrated about 1200 plants following a taxonomic sequence. This manuscript documents both the teaching methods of Pontedera and the plant collections cultivated in the Garden at that time. A latin manuscript by Giuseppe Antonio Bonato (Prefect from 1794 to 1835) contains the full text of the lessons of "Ostensio simplicium" held in 1795, revealing very innovatory contents such as the binomial plant names and the use of a phenological approach instead of a taxonomic one in dealing with the about 700 plants. Three italian manuscripts by Bonato contain the full text of his lessons of "Botanica", probably held in 1820-21, dealing with hystology, anatomy, morphology of vegetative and reproductive organs, as well as the systems and methods of classification available at that time. During his lessons, Bonato made use of more than 100 tables, intentionally painted by Luigi Pizzi to support Bonato’s teaching. Besides documenting the course contents, these manuscripts bring to light the Bonato’s impressive cultural background and teaching qualities.