We analyze the role and influence of a tradition of research linked to the concept of "primary matter" in nineteenth-century studies on the nature of the elements. The suggestion of William Prout in 1816 that the atomic weights of pure chemical elements are whole numbers and multiples of the atomic weight of hydrogen, taken as unity, was met with serious confutations, which in turn prompted several attempts to save Prout's hypothesis. We discuss these attempts in detail and the objections raised against them, for instance by Dmitry Ivanovich Mendeleev . We pay particular attention to the use of spectroscopy as a method for proving the existence of elementary forms of matter inside atoms. Leaders in this field of research were two English scientists, the astrophysicist Norman Lockyer (1836-1920) and the chemist William Crookes (1832-1919). Both of their approaches involved the idea of primary matter. However, while Crookes's approach proved to be incorrect, Lockyer's ideas survived for several years and supported the discovery of the electron by J.J. Thomson (1856Thomson ( -1940. nine years later was awarded the Nobel Prize in Physics for his work on the conduction of electricity through gases, introduced a new concept of matter: on this view we have in the cathode rays matter in a new state, a state in which the subdivision of matter is carried very much further than in the ordinary gaseous state: a state in which all matter-that is, matter derived from different sources such as hydrogen, oxygen, etc.-is of one and the same kind; this matter being the substance from which all the chemical elements are built up. 1