<i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i> are among the most commonly isolated bacterial species implicated as etiological agents of dental caries. Details of the composition of the oral microflora related to dental caries should aid in assessing the prevalence and risk of disease at an individual level. The aim of the present study was to determine the presence and relative amounts of <i>S. mutans</i> and <i>S. sobrinus </i>in the saliva samples obtained from schoolchildren in Khartoum State, the Sudan, and to study the association of the amounts of <i>S. mutans</i> and <i>S. sobrinus</i> with caries experience, socioeconomic status and sugar-sweetened snacks in this population. 140 samples, 30 of which were from individuals with caries experience, were examined using quantitative real-time polymerase chain reaction (qRT-PCR) with specific oligonucleotide primers. The mean ratio of fold differences of <i>S. mutans </i>to<i> S. sobrinus</i> was 0.77 (SD 5.4) and 2.29 (SD 6.0) for samples obtained from caries-free and caries-active individuals, respectively. This suggested that the proportion of <i>S. sobrinus</i> was higher than <i>S.</i><i>mutans </i>in the caries-active group when compared to the caries-free group. An association was found between children with caries-active lesions and the frequent consumption of sticky desserts and higher socioeconomic status. <i>S. sobrinus</i> seems to be associated with caries experience in the studied population. A proposal of caries screening programs designed to test for <i>S. sobrinus </i>in this population may be developed.