The emergence and inter-species dissemination of new tick-borne pathogens have become a serious health hazard in domestic animals. Ehrlichiosis caused by Ehrlichia (E.) ruminantium in small ruminants is becoming an emerging and prevailing issue adversely affecting the health and production of sheep and goats. The current study was designed to investigate the Ehrlichia infection load in the sheep and goat population of South Punjab, Pakistan. The phylogenetic analysis of local isolates along with risk factor analysis and comparative hematological analysis was also conducted. A total of 192 blood samples consisting of sheep (n=96) and goat (n=96) were subjected to microscopy and PCR. The study results revealed an overall prevalence of 04.69 and 7.81% based on microscopy and PCR respectively. A higher molecular prevalence of Ehrlichia was observed in goats (9.38%) as compared to sheep (6.25%). The phylogenetic tree constructed by the maximum likelihood method exhibited the identity of study isolate with E. ruminantium isolated from various countries. The risk factor analysis showed a significant association of previous tick history, tick infestation, presence of shrubs, and tick control strategies adaptation with the disease occurrence. The hematological analysis observed a significant reduction in RBCs, hemoglobin, and hematocrit in infected animals compared to healthy animals. The study concludes that Ehrlichia infection is an emerging issue of small ruminants. The hematological findings can be helpful in early detection of disease in field conditions but molecular confirmation by PCR is necessary for accurate diagnosis of Ehrlichia infection while risk factor analysis will provide the relevant information to develop control measures for preventing the spread of disease.