Retinitis pigmentosa (RP) is a group of inherited retinal eye diseases caused by the gradual loss of the photoreceptor cells. The present study was initiated to elucidate the molecular characterization of inherited retinitis pigmentosum in Pakistani population. The relatively high degree of consanguinity in Pakistani families makes the population a valuable resource to investigate the genetic basis of autosomal recessive RP (arRP). To explore the pathogenic mutations responsible for arRP, 50 consanguineous families affected with arRP were identified and enrolled through Eye hospitals from Punjab and Sind provinces of Pakistan. After genomic DNA extraction from the white blood cells, an exclusion linkage analysis of 25 families for reported genes/loci were completed by short tandem repeat markers labeled with fluorescence. During exclusion analysis, seven families were found linked to reported genes and loci. Two families PKRP259 and PKRP268 were found linked with TULP1, one family PKRP262 was found linked with RP1, one family PKRP264 was linked with PDE6B, one family PKRP235 was found linked with RPE65 and two families PKRP031 and PKRP224 were found linked to chromosome 1p21.3-p13.3 harboring RP32 locus. Mutational analysis of these four genes identified a novel missense mutation (c.1561C>T; p.Pro521Ser) in PKRP259, a splice site mutation (c.1495+4A>C; p.Pro499Argfs104*) in PKRP268, a splice site mutation (c.787+1G>A; p.Ile263Asnfs8*) in PKRP262, a novel deletion mutation (c.243delG; p.Arg82Alafs68*) in PKRP264 and a novel deletion mutation (c.361delT; p.Ser121Leufs6*) in PKRP235. The next-generation whole-exome sequencing (WES) is a powerful technique for gene discovery and identification of pathogenic mutation. The WES of one affected member from family PKRP030 identified a missense mutation (c.75C>A; p.Asp25Glu) in the CLCC1 gene. Bi-directional Sanger sequencing of CLCC1 gene in two additional families (PKRP031 and PKRP224) identified the same missense mutation (c.75C>A; p.Asp25Glu) which was identified in family PKRP030 by WES.