Background: Herpes simplex virus Type 2 (HSV-2) has been associated with HIV infection. More recently, HSV-2 incidence has been linked to HIV acquisition. A few studies have suggested that the fishing communities have a high HSV-2 prevalence but there is limited knowledge on HSV-2 incidence and associated risk factors among fishermen. Methods: Three hundred fishermen were consented, and evaluated for baseline HSV-2 serology status and again after 12 months among those negative at baseline. Sexual behavior and socio-demographic data were collected at enrolment and exit visits using a structured questionnaire. Baseline HIV serology and Human papillomavirus (HPV) DNA genotyping were also performed. Multivariate logistic regression was used to determine independent factors associated with HSV-2 acquisition. Results: Baseline HSV-2 prevalence was 56.3% (95% CI: 50.7 - 62.0). Factors associated with HSV-2 prevalence were, older age (aOR = 1.96; 95% CI: 1.16 - 2.85), history of STI (aOR 2.12; 95% CI: 1.19 - 3.91), infection with HIV (aOR 2.22; 95% CI: 1.17 - 4.22), ever married (aOR = 3.80; 95% CI: 1.42 - 11.90), most recent sexual act with sex worker/casual partner (OR= 3.56; 95% CI: 1.49 - 8.62) and inconsistent condom use with new sexual partner (aOR = 6.34; 95% CI: 2.24 - 13.04). The HSV-2 incidence was 23.6 (95% CI = 15.4 - 31.8)/100 pyr. Infection with persistent high-risk (HR) HPV (aIRR = 3.35; 95% CI: 1.21 - 11.37), multiple (≥2) partners in 12 months prior to study participation (aIRR = 4.77; 95% CI: 1.12 - 11.38), inconsistent condom use with new partner (aIRR =2.53; 95% CI: 1.12 - 7.38) and most recent sexual act with sex worker/casual partner (OR = 3.03; 95% CI: 1.17 - 8.58) were independent risk factors for HSV-2 acquisition. Conclusion: The incidence of HSV-2 is very high among fishermen. It is associated with persistent HR HPV infection and high-risk sexual behavior. Intervention strategies targeting these men with high risk sexual behavior are urgently needed to stop new HSV-2 acquisition and subsequently prevent HIV infection.