Ultrathin FeSe films grown on SrTiO$_{3}$ substrates are a recent milestone in atomic material engineering due to their important role in understanding unconventional superconductivity in Fe-based materials. Using femtosecond time- and angle-resolved photoelectron spectroscopy, we study phonon frequencies in ultrathin FeSe/SrTiO$_{3}$ films grown by molecular beam epitaxy. After optical excitation, we observe periodic modulations of the photoelectron spectrum as a function of pump-probe delay for 1 unit cell, 3 unit cell, and 60 unit cell thick FeSe films. The frequencies of the coherent intensity oscillations increase from 5.00(2) to 5.25(2) THz with increasing film thickness. By comparing with previous works, we attribute this mode to the Se A$_textrm{1g}$ phonon. The dominant mechanism for the phonon softening in 1 unit cell thick FeSe films is a substrate-induced lattice strain. Our results demonstrate an abrupt phonon renormalization due to a lattice mismatch between the ultrathin film and the substrate.
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