This chapter discusses the methods for several important techniques for looking at plant chromosomes by transmission electron microscopy. It examines the chromosomes by thin-section electron microscopy, DNA:DNA in situ hybridization to sections, and transfer of spread chromosome preparations from the light to transmission electron microscope. As in light microscopy, many developments in electron microscopy have come into widespread use in botanical laboratories since 1980. New instruments are microcomputer controlled and hence much easier to use, with such developments as automatic focusing; simplified correction of astigmatism; simple photography; continuous, nonrotating zoom magnification controls; very low magnification for specimen finding; and long-life, stable, field-emission filaments. Plant research require anything to be examined by thin section electron microscopy, ranging from the hardest silica deposits in leaves to the structure of waxes or air spaces. The chemicals used in electron microscopy include highly toxic substances.