The crystal structure of naturally occurring zaccariniite from Loma Peguera (Republica Dominicana) has been studied in Transmission Electron Microscopy(TEM) with variable angle Precession Electron Diffraction (PED) techniques: 0.7° Precession Electron Diffraction Tomography (Precession EDT) for unit cell and Laue class sorting, 0.5° Scanning Precession Diffraction (SPED) for crystal orientation mapping and grain alignment, and high symmetry zone axis 1.2° to 2.2° Zone Axis High Angle Precession Electron Diffraction (ZA high angle PED) for Space Group assessment and supercell information gathering. The natural sample has been prepared into an electron thin lamella by means of Focused Ion Beam(FIB). The analysis of the data has yielded tetragonal cell parameters of 3.86, 3.86, 6.77 Å and space group of P4/nmm for the basic structure, and its constituent atom positions for Ni, As and Rh were determined as well by ab-initio structure resolution method in accordance to the elemental composition of the natural zaccariniite obtained with Energy Dispersive X-ray (EDX) and High Magnification Electron Microscopy (HMEM) analysis. A modulation of the crystal basic structure of 3 by 1 in the basal plane has been reported for the first time on natural occurring zaccariniite.