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This study investigates the interaction between emblematics and natural history, focusing on sixteenth- century botanical emblem books, in which plants can be seen as means of meditation. In the second half of the sixteenth century, the two genres of emblematics and natural history became so closely related that the empirical knowledge of natural history provided the reader a key for uncovering the disguised meaning of emblems. In particular, botanical emblem books, which appeared in the mid sixteenth century, demonstrate the combination of close scientific observations of plants and devotional approach to nature as God’s divine creation. This didactic and meditational use of botanical emblems is most evident in three botanical emblem books by Joris Hoefnagel (1542–1601), Joachim Camerarius the Younger (1534–98), and Thomas Palmer (1540–1626). In these books, Hoefnagel, Camerarius and Palmer demonstrated their emblematic way of looking at plants as an aid to meditation as well as their botanical knowledge in detail and accuracy, encouraging the audience to appreciate fully both the aesthetic beauty and the symbolic and allegoric meaning represented by each plant. Thus, these botanical emblem books represent their distinctive worldview of the late sixteenth century, with its combination of art, science, and emblematics.