South Sudan, like all other East African Countries through Global Fund had implemented severalrncontrol programs as per recommendation of WHO and succeeded to reduce malaria transmission fromrnintense to interrupted transmission contributing to the implementation of the elimination/eradicationrnprogram in the years to come. Investigation of the transmission pattern of the hotspot foci andrnunderstanding the dynamics of malaria transmission was essential. Therefore, this study planned Hotspotrnstudy on urban epidemiological setting of Wau town/city. Cross sectional studies of the town at 2rnmonths intervals in the dry season and two others in wet season were planned. Sample size wasrndetermined, peripheral blood Smear and RDT serological methods were adopted as standard methods ofrnprevalence study, positive in both were considered for determination of the prevalence. Accordingly,rnfour (4) study sites were selected and data collection was completed in Hai Nazareth, just before thernunpredicted war between the rebel and the government forces broke in the town. Hence, relying on onerntime cross sectional study for prevalence study and the retrospective data of the preceding year, 2015,rntaken from Health clinics and hospitals to establish the parasite prevalence. There was transmissionrnthroughout the year and an increase in all age groups in the rainy seasons between June and Octoberrnwith peak August-October. Infected individuals who visited the hospital and were found positive arernlarger in number in the age groups 6-15 and above 15. The result showed that 35% of infection in thosernunder 5 years is greater than 23% of those between 6-10 years indicating that the under 5 are the highrnrisk groups. The 16.1% in those under 1 year are most vulnerable for at that age they do not havernprotective immunity ready yet. P. falciparum was the only species diagnosed, accounting for 47.51% ofrnall subjects who visited for any other infections (52.49%), suggesting the health significance of Malariarnin the population. Primary data done in May and June showed 32.6% infection rate in the samplernpopulation of which 5.2% were children under 5 while the age groups 6-15 and above 15 years had 13rnand 14.4% respectively. All were asymptomatic cases. Given the retrospective study that showed a yearrnround transmission with a peak between June and October and then a decline to lowest level inrnDecember, the Frequency of infection in Children and age group below 15 is a high level of infectionrnand above 15 had relatively higher infection. The demographic distribution of the study population,rnMetrological data of the town, age distribution of the parasite prevalence, identification of major andrnminor vectors were also reflected and their implications in breaking transmission were discussed.rnKeywords: Hotspot foci, elimination, epidemiological setting, asymptomatic cases, parasite prevalence.