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Henslow graduated in 1818. He already had a passion for natural history from his childhood, which largely influenced his career, and he accompanied Sedgwick in 1819 on a tour in the Isle of Wight where he learned his first lessons in geology. He also studied chemistry under Professor James Cumming and mineralogy under Edward Daniel Clarke. In the autumn of 1819 he made valuable observations on the geology of the Isle of Man (Trans. Geol. Soc., 1821) and in 1820 and 1821 he investigated the geology of parts of Anglesey, the results being printed in the first volume of the Transactions of the Cambridge Philosophical Society (1822), the foundation of which society was originated in November 1819 by a group at Cambridge with Professors Farish, Lee, and Sedgwick and Henslow (at that time not yet a professor). The idea and initial impetus for the Society originated from Sedgwick and Henslow.

Meanwhile, Henslow had studied mineralogy with considerable zeal, so that on the death of Clarke he was in 1822 appointed Professor of Mineralogy in the University of Cambridge. Two years later he took holy orders. Botany, however, had claimed much of his attention, and to this science he became more and more attached, so that he gladly resigned the chair of Mineralogy in 1827, two years after becoming Professor of Botany. As a teacher both in the classroom and in the field he was eminently successful. He was a correspondent of John James Audubon who in 1829 named Henslow's Sparrow after him.

From 1821 Henslow had begun organising a herbarium of British flora, supplementing his own collecting with a network which expanded over time to include his friends and family, and the botanists William Jackson Hooker and John Hutton Balfour, as well as about 30 of his students. As a mineralogist he had used Haüy's laws of crystallography to analyse complex crystals as transformations of "the primitive form of the species" of crystal, and when he moved to botany in 1825 he sought similarly precise laws to group plant varieties into species, often including as varieties plants that respected taxonomists had ranked as separate species. He followed the understanding of the time that species were fixed as created but could vary within limits, and hoped to analyse these limits of variation. By a method he called "collation", Henslow prepared sheets with several plant specimens, each labelled with the collector, date and place of collection, comparing the specimens to show the variation within the species. His A Catalogue of British Plants was first published in October 1829, and became a set book for his lecture course. Earlier that year, Charles Darwin joined the course and along with other students helped to collect plants of Cambridgeshire. In 1830 Henslow experimented on varying the conditions of garden grown wild plants to produce various forms of the plant. In 1835 Henslow published Principles of Descriptive and Physiological Botany as a textbook based on this lecture course.

In the summer of 1831 Henslow was offered a place as naturalist to sail aboard the survey ship HMS Beagle on a two-year voyage to survey South America, but his wife dissuaded him from accepting. Seeing a perfect opportunity for his protégé, Henslow wrote to the ship’s captain Robert Fitzroy telling him that Darwin was the ideal man to join the expedition team. During the voyage, Darwin corresponded with Henslow, and collected plants with him in mind. In particular, when first arriving at the Galápagos Islands Darwin noted "I certainly recognize S America in Ornithology, would a botanist?", and went on to collect plant specimens carefully labelled by island and date. He also labelled the mockingbirds he caught, and initially thought these were varieties but while arranging these bird specimens on the last lap of the voyage he began wondering if they could be species, a possibility which would "undermine the stability of Species". Henslow's teaching continued to influence Darwin's work on evolution.

Besides Darwin, other famous students of Henslow included Berkeley, Babington, Lowe and Miller. Henslow founded the Cambridge University Botanic Garden in 1831. During his time at Cambridge he extended the Botanic Garden and remodelled the 40-acre site between Bateman Street and Brooklands Avenue, making it world-renowned.