The updated H-band spectral line list (from 15,000 - 17,000 Å) adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) for the SDSS IV Data Release 16 (DR16) is presented here. The APOGEE line list is a combination of atomic and molecular lines with data from laboratory, theoretical, and astrophysical sources. Oscillator strengths and damping constants are adjusted using high signal-to-noise, high-resolution spectra of the Sun and alpha Boo (Arcturus) as "standard stars". Updates to the DR16 line list, when compared to the previous DR14 version, are the inclusion of molecular H2O and FeH lines, as well as a much larger (by a factor of ~4) atomic line list, which includes significantly more transitions with hyperfine splitting. More recent references and line lists for the crucial molecules CO and OH were used, as well as for C2 and SiH. In contrast to DR14, DR16 contains measurable lines from the heavy neutron-capture elements cerium (as Ce II), neodymium (as Nd II), and ytterbium (as Yb II), as well as one line from rubidium (as Rb I), that may be detectable in a small fraction of APOGEE red giants.