Globally, Border disease virus (BDV) has caused substantial economic losses among small ruminants (sheep and goats). This is the first molecular study carried out in Mosul city, Iraq. To determine the prevalence of Border Disease Virus and to examine problem of persistent infection (PI) using Reverse transcriptase polymerase chain reaction technique (RT-PCR) in female local breed of small ruminants. During the period between November 2018 to June 2019, 364 blood samples were collected from 264 local Awassi sheep and 100 local cross breed goats secure provided by private breeders. The animals were of ≥1.5 years old and the samples were obtained from various locations in Mosul city, with varying rearing methods and had not been vaccinated against BDV. This investigation indicated that the prevalence of BDV infection in sheep and goats were 15.9% (42/264) and 3% (3/100) respectively, whereas the occurrence of PI in sheep was 2.38% and in goats was 0%. Hence it was concluded that Border disease was circulating in small ruminants in Mosul city. This calls for a need to design programs to monitor and control the disease and eventually eradicate it is prevalence in Mosul city.