Observations of the Pluto-Charon system, acquired with the ALMA interferometer on June 12–13, 2015, have led to the detection of the CO(3-2) and HCN(4-3) rotational transitions from Pluto (including the hyperfine structure of HCN), providing a strong confirmation of the presence of CO, and the first observation of HCN in Pluto’s atmosphere. The CO and HCN lines probe Pluto’s atmosphere up to ∼450 km and ∼900 km altitude, respectively, with a large contribution due to limb emission. The CO detection yields (i) a much improved determination of the CO mole fraction, as 515 ± 40 ppm for a 12 μbar surface pressure (ii) strong constraints on Pluto’s mean atmospheric dayside temperature profile over ∼50–400 km, with clear evidence for a well-marked temperature decrease (i.e., mesosphere) above the 30–50 km stratopause and a best-determined temperature of 70 ± 2 K at 300 km, somewhat lower than previously estimated from stellar occultations (81 ± 6 K), and in agreement with recent inferences from New Horizons / Alice solar occultation data. The HCN line shape implies a high abundance of this species in the upper atmosphere, with a mole fraction >1.5 × 10−5 above 450 km and a value of 4 × 10−5 near 800 km. Assuming HCN at saturation, this would require a warm (>92 K) upper atmosphere layer; while this is not ruled out by the CO emission, it is inconsistent with the Alice-measured CH4 and N2 line-of-sight column densities. Taken together, the large HCN abundance and the cold upper atmosphere imply supersaturation of HCN to a degree (7–8 orders of magnitude) hitherto unseen in planetary atmospheres, probably due to a lack of condensation nuclei above the haze region and the slow kinetics of condensation at the low pressure and temperature conditions of Pluto’s upper atmosphere. HCN is also present in the bottom ∼100 km of the atmosphere, with a 10−8–10−7 mole fraction; this implies either HCN saturation or undersaturation there, depending on the precise stratopause temperature. The HCN column is (1.6 ± 0.4)× 1014 cm−2, suggesting a surface-referred vertically-integrated net production rate of ∼2 × 107 cm−2 s−1. Although HCN rotational line cooling affects Pluto’s atmosphere heat budget, the amounts determined in this study are insufficient to explain the well-marked mesosphere and upper atmosphere’s ∼70 K temperature, which if controlled by HCN cooling would require HCN mole fractions of (3–7) ×10−4 over 400–800 km. We finally report an upper limit on the HC3N column density (<2 × 1013 cm−2) and on the HC15N / HC14N ratio (<1/125).