For the first time, transmission digital holography microscopy is applied to observe coal palynofacies, which are organic fossil microcomponents contained in the coal grains. The recorded holograms were produced by using microscope lenses with 20x and 40x of lateral magnification respectively, and He-Ne laser of wavelength 594.5 nm. The results show that reflection digital holography microscopy is required for observing relative opaque particles, because the phase recovery is strong diminished by light transmission in those cases. On the other hand, the phase distribution is related to the relief of the particles and the variations of their refraction index. Therefore, a priori information should be necessary to properly relate the phase information to physical features of the particles. Numerical unwrapping procedures are also crucial. Procedures with special requirements can be needed for analysing fast varying phase distributions. However, digital holography microscopy becomes a high performance tool for 3D modelling of fossil particles if the above requirements are enough fulfilled.