Somatosensory neurons are classified into three main types according to their modalities: nociceptive, thermal, and mechanosensory. Within each modality group, neurons can be further divided into morphologically and functionally distinct subclasses. Here we show that heparan sulfate D-glucosaminyl 3-O-sulfotransferase 2 (HS3ST-2) is a marker for specific subsets of TrkC-expressing cutaneous low-threshold mechanosensory and proprioceptive mechanosensory neurons. Two-color in situ analysis revealed that almost all HS3ST-2 signals colocalized with TrkC but not with TrkA or TrkB mRNA. To visualize the morphological subtypes of HS3ST-2/TrkC-expressing neurons, we generated a HS3ST-2-hPLAP knock-in mouse line, in which HS3ST-2-expressing neurons and their projections are labeled by human placental alkaline phosphatase (hPLAP). AP staining in these mice demonstrated that sensory endings of muscle spindles and Golgi tendon organs as well as the cutaneous mechanosensory Merkel and longitudinal lanceolate endings in the whiskers are strongly positive for hPLAP activity. In contrast, no nociceptive endings are labeled. In the glabrous and hairy skin, rare Merkel endings and transverse lanceolate endings are weakly stained. During development, each type of nerve endings forms at different time point. Muscle innervations differentiate first, followed by formation of cutaneous sensory endings. Our results revealed the subtype identities of TrkC-positive mechanosensory neurons and demonstrated the usefulness of HS3ST-2 as a genetic marker for these subclasses of neurons. J. Comp. Neurol. 511:543–556, 2008. © 2008 Wiley-Liss, Inc.