Soon he began travelling around France and went several times to Paris where he met Pierre André Latreille who suggested to specialize on Diptera, following the pioneering work of Johann Wilhelm Meigen.
After some time in Holland he married and moved from Hazebrouck to Lestrem where he became mayor, from 1817 to 1852, then a member of the Conseil général of Pas-de-Calais.
His early taxonomic work included the Insectes diptères du nord de la France, published in Lille in 4 parts from 1826-1829.
This arrangement was continued by Nicolas Roret when Latreille became ill. Two volumes were published (1834-1835) as Histoire naturelle des insectes Dipteres where non-European as well as European Diptera were treated.
In 1839, Macquart visited Johann Wilhelm Meigen, then aged 75, in Stolberg, purchasing his notes and drawings and bringing his collection to Paris where it is now in the Muséum national d'histoire naturelle.
He described nearly 2,000 new species in his Insectes diptères exotiques nouveaux ou peu connus (1838–1855) which lists the collections examined to that date.
They are those of: Jules Dumont d'Urville with René-Primevère Lesson (the largest including material from the Falkland Islands, the coast of Chile and Peru, the southern and western Pacific, Australia, New Zealand and New Guinea); Justin Goudot who had explored South America from 1822 (and continued to until 1842); a Louis Pilate who was based in Georgia and Louisiana U.S.A. but lived for five years in Mérida, Yucatán; Auguste Sallé, a young collector later to become a Paris insect dealer with South American connections; Alcide Charles Victor Marie Dessalines d'Orbigny who between 1826 and 1823 had travelled, on a mission for the Paris Museum, into Brazil, Argentina, Paraguay, Chile, Bolivia and Peru returning France with an enormous collection of more than 10,000 natural history specimens; Peter Claussen (c. 1804–1855) a Danish naturalist who collected in Brazil, a M. Giesebrecht, Étienne Geoffroy Saint-Hilaire (Diptera from Egypt) and three members of a Belgian Commission for the exploration of tropical countries, August Giesebreght (1810–1893), Nicholas Funk (1817–1896) and Jean Jules Linden (1817–1898).