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Polypyrrole-based polyamides are used as sequence-specific DNA probes. However, their cellular uptake and distribution are affected by several factors and have not been extensively studied in vivo . Here, we generated a series of fluorescence-conjugated polypyrrole compounds and examined their cellular distribution using live zebrafish and cultured human cells. Among the evaluated compounds, Py 3 -FITC was able to visualize collagen-rich tissues, such as the jaw cartilage, opercle and bulbus arteriosus, in early-stage living zebrafish embryos. Then, we stained cultured human cells with Py 3 -FITC and found that the staining became more intense as the amount of collagen was increased. In addition, Py 3 -FITC-stained HR cells, which represent a type of ionocyte on the body surface of living zebrafish embryos. Py 3 -FITC has low toxicity, and collagen-rich tissues and ionocytes can be visualized when soaked in Py 3 -FITC solution. Therefore, Py 3 -FITC may be a useful live imaging tool for detecting changes in collagen-rich tissue and ionocytes, including their mammalian analogues, during both normal development and disease progression.