Infections caused by arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) frequently occur in tropical and subtropical regions. These three viruses are transmitted by Aedes (Ae.) aegypti and Ae. albopictus. In Thailand, the highest incidence of arbovirus infection and the high circulation of Aedes mosquito mainly occurs in the Southern provinces of the country. Few studies have focused on the incidence of co-infection of arboviruses in this region. In the present study, a cross-sectional study was conducted on a cohort of 182 febrile patients from three hospitals located in Southern Thailand. Surveillance of DENV, CHIKV and ZIKV was conducted from May to October 2016 during the rainy season. The serological analysis and molecular detection of arboviruses were performed by ELISA and multiplex RT-PCR respectively. The results demonstrated that 163 cases out of 182 patients (89.56%) were infected with DENV, with a predominance of DENV-2. Among these DENV positive cases, a co-infection with CHIKV for 6 patients (3.68%) and with ZIKV for 1 patient (0.61%) were found. 19 patients out of 182 were negative for arboviruses. This study provides evidence of co-infection of arboviruses in Southern Thailand and highlight the importance of testing DENV and other medically important arboviruses, such as CHIKV and ZIKV simultaneously.