Electron phase space holes (EHs) associated with electron trapping are commonly observed as bipolar electric field signatures in both space and laboratory plasma. Until recently, it has not been possible to resolve EHs in electron measurements. We report observations of EHs in the plasma sheet boundary layer, here identified as the separatrix region of magnetic reconnection in the magnetotail. The intense EHs are observed together with an electron beam moving toward the X line, showing signs of thermalization. Using the electron drift instrument onboard the satellites of the Magnetospheric Multiscale mission, we make direct millisecond measurements of the electron particle flux associated with individual electron phase space holes. The electron flux is measured at a millisecond cadence in a narrow parallel speed range within that of the trapped electrons. The flux modulations are of order unity and are direct evidence of the strong nonlinear wave-electron interaction that may effectively thermalize beams and contribute to transforming directed drift energy to thermal energy.