Endosymbionts such as bacteria and fungi play crucial roles in the survival and growth of host plants. The identification of these microorganisms often requires a combination of traditional staining methods, such as Gram staining, and the use of complex microscopy such as scanning electron microscope. Microscopic techniques, including light, fluorescence, confocal, and electron microscopy, provide insights into endosymbionts’ morphology, localization, and structure within the host tissues. This chapter outlines the protocols for the morphological examination and microscopic visualization of endosymbionts.