The desmitracheate system in a “micronetine” genus Nippononeta Eskov, 1992 is recognized for the first time in the present study. This makes the subfamilial placement of this genus problematic. A morphological study was conducted for Nippononeta kurilensis Eskov, 1992 (the type species of Nippononeta) and Nippononeta coreana (Paik, 1991). Characters of genitalia and tracheal system, as well as some somatic characters were studied in detail by using scanning electronic microscopy (SEM), and compared with those of Agyneta. Updated descriptions of the genus Nippononeta and its two species are presented. Putative synapomorphies for Nippononeta and Agyneta are provided, as well as some putative synapomorphies shared by the two genera. The results imply that both scaped epigynum and desmitracheate tracheal system are probably homoplastic. The placement of Nippononeta and Agyneta within Linyphiidae need to be resolved in future studies.