The transport of germ cells from the base of the seminiferous epithelium towards the luminal edge of the tubule lumen in the adluminal compartment during the epithelial cycle is an essential cellular event to support spermatogenesis. Thus, fully developed elongated spermatids (i.e., spermatozoa) can be released at spermiation in late stage VIII in rodents versus late stage II in humans. Earlier studies to examine the molecular mechanism(s) that support germ cell transport, most notably the transport of preleptotene spermatocytes across the blood-testis barrier (BTB), and the transport of elongating spermatids across the adluminal compartment during spermiogenesis, is focused on the adhesion protein complexes at the cell-cell interface. It is generally accepted that cell junctions at the Sertoli cell-cell interface at the BTB, including the actin-based tight junction (TJ), basal ectoplasmic specialization (basal ES, a testis-specific adherens junction) and gap junction (GJ), as well as the intermediate filament-based desmosome undergo constant remodeling to accommodate the transport of preleptotene spermatocytes across the barrier. On the other hand, similar junction dynamics (i.e., disassembly, reassembly and stabilization/maintenance) take place at the Sertoli-spermatid interface. Emerging evidence has shown that junction dynamics at the Sertoli cell-cell vs. Sertoli-germ cell interface are supported by the two intriguingly coordinated cytoskeletons, namely the F-actin- and microtubule (MT)-based cytoskeletons. Herein, we provide a brief summary and critically evaluate the recent findings. We also provide an updated hypothetical concept regarding germ cell transport in the testis utilizing the MT-conferred tracks and the MT-specific motor proteins.