Local circuit GABAergic interneurons comprise the most diverse cell populations of neuronal networks. Interneurons have been characterized and categorized based on their axo-somato-dendritic morphologies, neurochemical content, intrinsic electrical properties and their firing in relation to in-vivo population activity. Great advances in our understanding of their roles have been facilitated by their selective identification. Recently, we have described three major subtypes of deep short-axon cells (dSACs) of the main olfactory bulb (MOB) based on their axo-dendritic distributions and synaptic connectivity. Here, we investigated whether dSACs also display pronounced molecular diversity and whether distinct dSAC subtypes selectively express certain molecules. Multiple immunofluorescent labeling revealed that the most commonly used molecular markers of dSACs (e.g. vasoactive intestinal polypeptide, calbindin and nitric oxide synthase) label only very small subpopulations (< 7%). In contrast, voltage-gated potassium channel subunits Kv2.1, Kv3.1b, Kv4.3 and the GABAA receptor α1 subunit are present in 70–95% of dSACs without showing any dSAC subtype-selective expression. However, metabotropic glutamate receptor type 1α mainly labels dSACs that project to the glomerular layer (GL-dSAC subtype) and comprise ∼20% of the total dSAC population. Analysing these molecular markers with stereological methods, we estimated the total number of dSACs in the entire MOB to be ∼13 500, which is around a quarter of the number of mitral cells. Our results demonstrate a large molecular heterogeneity of dSACs and reveal a unique neurochemical marker for one dSAC subtype. Based on our results, dSAC subtype-specific genetic modifications will allow us to decipher the role of GL-dSACs in shaping the dynamic activity of the MOB network.