The fibrous structures of collagen provide physical strength and stability to tissues and organs. Abnormalities in their orientation, growth, and remodeling cause morphogenetic defects and serious diseases including fibrosis, so it is important to clarify how collagen fibers are correctly oriented and grown within tissues. However, this mechanism remains elusive, as few methods have been available to fluorescently stain collagen fibers with a simple protocol and to observe their structure in three dimensions. Here we present a facile method that enables fluorescent staining of collagen fibers in vertebrate tissues. In our method using DAF-FM, known as a NO detection probe, premature collagen fibers can be visualized via covalent binding to the allysine residues serving as precursors of cross-linking structures of collagen. In addition, we showed that the labeling method using two fluorescent probes with different colors, DAF-FM and DAR-4M, allows for pulse-chase observation of newly synthesized collagen fibers. Our method will be a breakthrough technique in future collagen studies.