A new species of small water strider (Hemiptera: Heteroptera: Veliidae), Microvelia pilosa sp. nov., is described from Aichi Prefecture, Honshu, Japan. It belongs to the subgenus Picaultia Distant, 1913 within the genus Microvelia Westwood, 1834, and is similar to Microvelia japonica Esaki and Miyamoto, 1955 and Microvelia douglasi douglasi Scott, 1874. The new species can be distinguished from these two taxa by its blackish-brown body, small punctures on the pronotum, and arcuate right paramere that is slender only in the distal part. Our molecular phylogenetic analysis using the mitochondrial COI gene revealed that M. pilosa sp. nov. is genetically separated from some of the other Japanese Microvelia and is most closely related to M. japonica.