Rodrigues initially became a teacher of drawing at the Colegio Pedro II who specialized in botany, under the supervision of Francisco Freire Allemão e Cysneiro. He began his botanical expeditions in 1868 and was commissioned by the Brazilian government in 1871 to explore the Amazon basin and study palms, in part due to sponsorship by Guilherme Schüch, Baron of Capanema. This expedition lasted more than three years, during which time which he drew not only plants but also animals and Indian artefacts. By the early 1890s, he had created nearly 900 color plates of Brazilian orchids. Because of difficulty financing a publication with illustrations, Rodrigues published descriptions of more than 540 new orchids and 28 new genera without any images in his important two-volume work "Genera et species orchidearum novarum" (1877/1881). He then allowed another botanist, Alfred Cogniaux, to publish black-and-white versions of some 260 of his drawings in Cogniaux's "Flora Brasiliensis" (1893–1906). Nearly one-third of the species included in "Flora Brasiliensis" were initially described by Rodrigues.