Abstract Severe side effects from chemotherapy or immunotherapy often limit their clinical utility in urothelial cell carcinoma of the bladder. To explore alternative therapies, we were particularly interested in one of medicinal mushrooms called Phellinus linteus (PL) with antitumor/anticancer activity. We investigated possible anticancer effects of three distinct extracts or fractions of PL using an urothelial cell carcinoma (UCC) model in vitro. Those fractions included PL-I (crude extract), PL-II (water-extracted), and PL-III (ethanol-extracted), which were tested for their antiproliferative effects on UCC cells. To explore the anticancer mechanism(s) of these fractions, cell cycle analysis and analyses of epigenetic parameters, caspases-3 and -9, and apoptotic regulators, were also performed. Both PL-I and -II induced a maximum growth reduction of ~60% at 700 μg/ml while PL-III led to a ~90% growth reduction at 150 μg/ml in 72 h. Cell cycle analysis indicated that cells treated with 500 μg/ml (IC50) of PL-I and -II or 60 μg/ml (IC50) of PL-III underwent a G1 cell cycle arrest, accompanied by the up-regulation of p21, a cell cycle-dependent kinase inhibitor. Additionally, histone deacetylase (HDAC) activity was significantly (>60%) lost, while both histones H3 and H4 were highly acetylated, indicating alterations in the chromatin structure. Moreover, both caspases-3 and -9 in cells treated with each IC50 of three PL-fractions were all significantly (p<0.03) activated, implying induction of apoptosis. The present study shows that all three PL-fractions, PL-I, -II, and -III, have anticancer effects on UCC cells, although PL-III appears to be the most potent. Such an anticancer mechanism is attributed to a p21-mediated cell cycle arrest with epigenetic modifications involving HDAC inactivation and hyperacetylation of H3 and H4, ultimately leading to apoptotic cell death. Therefore, PL-fractions may have clinical implications in a safer and improved therapeutic modality for urothelial cell carcinoma.