A pair of laminar, premixed, CH4–O2 flames above 2000 K at atmospheric pressure, one fuel-rich (FR) and the other fuel-lean (FL), were doped with ~10−6 mol fraction of the second-row transition metals Y, Zr, Nb, and Mo. Since these hydrocarbon flames contain natural ionization, metallic ions were produced in the flames by the chemical ionization (CI) of metallic neutral species, primarily by H3O+ and OH− as CI sources. Both positive and negative ions of the metals were observed as profiles of ion concentration versus distance along the flame axis by sampling the flames through a nozzle into a mass spectrometer. For yttrium, the observed ions include the YO+•nH2O (n = 0–3) series, and Y(OH)4−. With zirconium, they include the ZrO(OH)+•nH2O (n = 0–2) series, and ZrO(OH)3−. Those observed with niobium were the cations Nb(OH)3+ and Nb(OH)4+, and the single anion NbO2(OH)2−. For molybdenum, they include the cations MoO(OH)2+ and MoO(OH)3+, and the anions MoO3− and MoO3(OH)−. Not every ion was observed in each flame; the FL flame tended to favour the ions in higher oxidation states. Also, flame ions in higher oxidation states were emphasized for these second-row transition metals compared with their first-row counterparts. Some ions written as members of hydrate series may have structures different from those of simple hydrates; e.g., YO+•H2O = Y(OH)2+ and ZrO(OH)+•H2O = Zr(OH)3+, etc. The ion chemistry for the production of these ions by CI in flames is discussed in detail. Keywords: transition metals, ions, flame, gas phase, negative ions.