Cresol red is a color marker and pH indicator for various laboratory procedures. As a color marker in agarose and polyacrylamide electrophoresis at 1% it runs at 125 base pair size, and as a titrant indicator Cresol Red is yellow below pH 7.2 and purple at pH 8.8 and above. Cresol Red can be used with Taq polymerase because it does not inhibit reactions unlike other dyes and has also been used as a pH sensitive optical fiber sensor.

p-Iodonitrotetrazolium Violet (also called INT) is a tetrazolium dye that turns purple upon reduction. INT dye is often used to visualize dehydrogenase activity histochemically as well as western blot staining and as a staining agent for soft agar colony formation assays.

Perylene is a polycyclic hydrocarbon. When used as a dye perylene displays a blue fluorescence, making it useful as a lipid probe in cytochemistry. It is also used in peroxyoxalate luminescence and has the strongest chemiluminescent response out of the fluorophores used. Perylene also forms the basis for the synthesis of several other dyes such as vat red 29.

Phenolphthalein disulfate is used in a broth as a substrate for arylsulfatase. This broth is a medium used to differentiate pathogenic mycobacteria based on their arylsulfatase production ability, those that produce arylsulfatase release phenolphthalein and, with the addition of an alkali, will turn the solution pink. The desulfuration of phenolphthalein disulfate was also used to isolate and identify intestinal bacteria.

Xylenol Blue is a useful alternative to thymol blue developed in the 1920s. Xylenol Blue can be used at half the concentration that thymol blue requires. It is functional at the same two pH ranges, acidic (pH 1-3), which transitions from red to yellow, and basic (pH 8-10), which transitions from yellow to blue. Xylenol Blue may be substituted for any experiment that requires thymol blue.