Konjac (Amorphophallus muelleri), a genus of tuberous plants in the Araceae family, is one of high-value crops in Southwest China. This study aimed at identifying the main pathogens causing tuber rot during storage of A. muelleri and screening the effective fungicides, so as to prolong the storage period of A. muelleri and decrease the losses. Isolation and identification, as well as pathogenicity test and retro-inoculation experiments were made for the pathogen causing tuber rot during storage of A. muelleri in Kunming city, Yunnan province, China. The effective fungicides for the main pathogens were also screened in the laboratory. Six fungi were identified as the pathogens causing tuber rot of A. muelleri, which were Fusarium solani (Mart.) Sacc., Fusarium oxysporum Schlecht., Botrytis cinerea Pers., Alternaria alternata (Fr.) Keissl., Rhizopus nigricans Ehrenb., Penicillium ulaiense Hsieh, Su & Tzean. The main pathogens causing postharvest diseases of A. muelleri were F. solani, F. oxysporum and B. cinerea. The isolation frequencies of them were 33.9%, 10.5% and 19.4%, respectively. After artificial inoculation, the incidence of tubers infected by F. solani, F. oxysporum and B. cinerea was 100%, 83% and 95%, respectively. The results of chemical screening showed that, in potato dextrose agar (PDA) media plate, the compounds Fludioxonil (50% WP) and Boscalid (50% WG) were the most effective in controlling the three main pathogens, and the average effect reached more than 97%. The test of fungicidal antisepsis on tubers consisted of A. muelleri being dipped in the 9,000 diluted solution of Fludioxonil (50% WP) or in the 3,500 diluted solution of Boscalid (50% WG) for 3 min and stored at room temperature (25 °C) for 7 d and 15 d, respectively. The fungicidal effects of Fludioxonil against F. solani, F. oxysporum and B. cinerea for 7 d and 15 d were 88.6%/83.2%, 90.1%/84.7% and 93.0%/91.5%, respectively, whereas the fungicidal effects of Boscalid were 87.0%/85.3%, 89.0%/85.6% and 89.2%/89.1%, respectively. The results may provide useful information for the control of postharvest diseases of A. muelleri.