Loeffler's Methylene Blue stain is used for the identification of diphtheria bacilli, since it differentiates the deeply stained metachromatic granules from the pale blue-staining cytoplasm and also as a counterstain in AFB staining

Malachite Green is used for bacterial spore staining by Schaeffer and Fulton's method. It can also used as a simple stain.

The Giemsa solutions contain methylene blue and eosin.These basic and acidic dyes induce multiple colours when applied to cells. The basic component of white cells (i.e. cytoplasm) is stained by acidic dye and they are described as eosinophilic or acidophilic.The acidic components (e.g. nucleus with nucleic acid) take blue to purple shades of the basic dyes and they are called basophilic. The neutral components of the cell are stained by both the dyes.