Streptococcus pyogenes is a gram positive pathogen causing pharyngitis, mild infections to chronic complications (Rheumatic Heart Disease, RHD). In this study, echocardiographic and clinical profile in pharyngitis, rheumatic fever patients were compared with virulent genes emm, spe A, spe B and sof. Nearly 107 subjects were classified into Group I – Pharyngitis (n=30), Group II – Rheumatic Fever (n=30) and Group III – healthy controls (n=47). The isolated S.pyogenes from Group I and Group II patient’s throat swab were subjected to 16S rRNA gene sequence. Multiplex PCR was done for identification of virulent genes. Electrocardiogram and Echocardiography was done for all the groups. For statistical analysis ANOVA and t-test were used. Comparison between groups were done by Tukey’s Multiple Comparison test. Among 107 isolates, 16.7% emm gene were detected in Group I and 23.3% in Group II, 56.67 % of spe B in Group I and 73.33 % in Group II, 36.67% of sof gene in Group I and 40% in Group II. Mitral Regurgitation was most commonly encountered in rheumatic fever. Hemoglobin (<0.001) and RDW (<0.001) was significantly lower in Rheumatic Fever whereas Platelet count (<0.001) and Neutrophil (<0.001) was significantly higher when compared with control subjects by Tukey’s Multiple Comparison test. When we compared the genetic relationship with the Echocardiographic findings, presence of one, two or three genes showed moderate to severe regurgitation in Rheumatic Fever subjects.