Methyl green stains DNA but it is not a specific dye of DNA. Used alone on whole cells, it stains almost everything and in particular the pectocellulosic wall. To increase its apparent specificity, it must be used with a complementary dye.

In the nucleus, the chromatin is stained with methyl green while the nucleoli are strongly stained with pyronine. Chromatin corresponds to interphase chromosomes, one of whose constituents is DNA. At the level of the nucleoli (without membrane) are gathered many molecules of RNA. These are rRNA molecules that are synthesized and assembled into ribosomal subunits at the level of the nucleoli.

The cytoplasm is also stained by pyronine. The pink beaches correspond to areas rich in rRNA, the participation of other RNAs (tRNA and mRNA) in the staining being practically anecdotal.