Crystallographic ordering and defects in WSe2 thin films with ultralow thermal conductivity are characterized by electron imaging and diffraction in cross-sectional geometry. The results show that the film consists of oriented, coherent crystallites that are a few nanometers in diameter. Two films of different thickness with different thermal conductivity are compared. We show that the film with a lower thermal conductivity is characterized by less coherent crystallites with a greater degree of misorientation.