The pygmy corydoras is a silver-colored fish, with an unbroken black line that runs horizontally along the center of the sides of the fish from the tip of its snout to its caudal peduncle.   It has a second thin black line along the lower part of the side of the body, from behind the ventral fins and continuing into the tail.  The top part of the body has a light black or dark gray shading that starts on the top of its snout and ends at the tail.  Newly hatched fry have vertical stripes along the sides of their bodies that fade by the end of their first month, when the horizontal stripes of the adult fish begin to appear.

Eggs of the fish are opaque, with a slight tan and opal color. Fry hatch after two or three days, and begin to develop coloration after about five days. They do not begin to resemble adults until about two weeks after hatching, when their body shape and barbels begin to become more pronounced.   After about one month, fry began to show their prominent black lateral line marking similar to their parents.

The maximum length of the species is about 3.2 centimeters (1.3 in), but typical adult sizes are 1.9 centimeters (0.75 in) for males and 2.5 centimeters (1.0 in) for females.  In addition to their larger length, females are also rounder and broader than males, especially when they have eggs.  Young fry grow rapidly after hatching, reaching 13 millimeters (0.51 in) in six to eight weeks.