Abstract The bean flower thrips, Megalurothrips usitatus Bagnall (Thysanoptera: Thripidae) is a major pest of leguminous crops grown in Southern China. This study reports the isolation, identification (through molecular characterization) and pathogenic potential of 6 fungal isolates belonging to different fungal species. The fungi were isolated from soil samples collected from different areas of Southern China and were identified as Beauveria bassiana (3 isolates; SB010, SB009, SP016), Cordyceps fumosorosea (one isolate; SP535), Akanthomyces attenuatus (one isolate; SCAUDCL-53), and Aspergillus nomius (one isolate; SCAUN-1). Conidial suspension (1 × 108 conidia ml−1), and the crude extract (0.4 mg ml−1) of all the 6 fungal isolates were tested for their pathogenicity against M. usitatus adults. The results showed that A. attenuatus (SCAUDCL-53) and B. bassiana (SB010) were the most effective fungal isolates against M. usitatus out of all the isolates used in this study. At 5 days post-inoculation, conidial suspension of A. attenuatus (SCAUDCL-53) and B. bassiana (isolate SB010) caused 100 and 90% mortality rates, respectively. The median lethal time (LT50) values of fungal isolates SCAUDCL-53, SB010, SB009, SP016, SP535, and SCAUN-1against M. usitatus adults were 1.36, 3.79, 6.51, 8.49, 17.36, and 5.01 days, respectively. The application of crude fungal extracts of SCAUDCL-53, SB010, SB009, SP016, SP535, and SCAUN-1 against the pest resulted in 85, 93.3, 56.7, 33.3, 41.7, and 53.75% mortality rates, respectively after 5 days of application. Respective LT50 values of the crude fungal extracts against M. usitatus were 3.37, 2.85, 4.87, 7.13, 6.43, and 4.64 days. The fungal isolates used in this study showed considerable bioactivity against the M. usitatus and can be used as potential natural pest control agent for the ecofriendly management of M. usitatus.