Paedocypris progenetica is distinguished from Paedocypris micromegethes by: a smaller maximum size (male 9.8mm, versus 11.6; female 10.3mm, versus 11.4), keratinized pad in front of male pelvic fins as a projecting knob (versus flat to slightly swollen), breeding tubercles on the dentary arranged in a straight row, without forming a cluster (versus forming a cluster of up to five closely set individual tubercles, subdistally on the lateral side of the dentary, supported by a conspicuous lateral bony extension), pelvic fins of female vestigial, or often missing (versus smaller than in male but similarly shaped), presence of pre-anal-fin-fold in female (a character unique among teleosts; versus absent in both sexes), dense small chromatophores in deep layer on abdomen appearing as a continuous patch, tiny black vermiculations on belly from throat to anus, including on male's pre-pelvic keratinized knob (versus large superficial, isolated chromatophores on belly from throat to anus, absent on male's keratinized pad), numerous small, contiguous chromatophores on middorsal line, organized in 3-5 rows, forming a broad stripe (versus few large isolated chromatophores, forming 1-3 irregular rows), pelvic-fin rays plain brown (versus with rows of spots).