HSV-2 is a common human pathogen that can cause primary and recurrent infection of the mucous membrane. Genital infection with HSV-2 facilitates the acquisition of HIV, both mutually reinforcing infection. Infection with herpes simplex virus type 2 is a significant public health problem being the leading cause of genital ulcerative disease. This study aimed at Molecular investigation and association of HIV and HSV-2 IgM co-infection among asymptomatic pregnant women in Port Harcourt, Nigeria. This is a cross-sectional study conducted at the antenatal unit of the University of Port Harcourt Teaching Hospital (UPTH), River State. A total of 168 consenting pregnant women were selected. The study involved collecting socio-demographic data and laboratory determination of HSV-2 immunoglobulin M (IgM) and HIV seroprevalence using enzyme linked immunosorbent assay (DIAPRO Diagnostic Bioprobes, Milan, Italy) and ALERE determine/STAT PAK respectively. Data analysis was done using graph pad statistical package. Chi square analysis was used to determine the correlation of the infection with socio-demographic factors. The seroprevalence for HSV-2 IgM was 29.8% (50/168) of the respondents while there was no co-infection between IgM and HIV. All HIV respondents were married. Majority are trader having tertiary educational qualification and are in a monogamous relationship. With regard to IgM seropositivity age, marital status, religion and gestation period were significantly associated with IgM while educational level, occupation, type of family and parity were not significantly associated with HSV-2 IgM. There is a significant correlation between HIV seropositivity with parity and history of sexually transmitted disease while there is no significant difference between HIV prevalence with age, marital status education level occupation type of family, religion history of abortion and the prevalence of HSV-2 was high among women of childbearing age in Port Harcourt, Nigeria. Effort should be made to increase the awareness of HSV-2 and HIV infection among the childbearing populace and serological testing of pregnant women should be included as a routine test.