BackgroundRetinitis Pigmentosa (RP) is a clinically and genetically progressive retinal dystrophy associated with severe visual impairments and sometimes blindness, the most common syndromic form of which is Usher syndrome (USH). This study aimed to further increase understanding of the spectrum of RP in the Khyber Pakhtunkhwa region of Pakistan.MethodologyFour consanguineous families of Pashtun ethnic group were investigated which were referred by the local collaborating ophthalmologists. In total 42 individuals in four families were recruited and investigated using whole exome and dideoxy sequencing. Among them, 20 were affected individuals including 6 in both family 1 and 2, 5 in family 3 and 3 in family 4.ResultPathogenic gene variants were identified in all four families, including two in cone dystrophy and RP genes in the same family (PDE6C;c.480delG, p.Asn161ThrfsTer33 andTULP1;c.238 C > T, p.Gln80Ter) with double-homozygous individuals presenting with more severe disease. Other pathogenic variants were identified inMERTK(c.2194C > T, p.Arg732Ter),RHO(c.448G > A, p.Glu150Lys) associated with non-syndromic RP, andMYO7A(c.487G > A, p.Gly163Arg) associated with USH. In addition, the reported variants were of clinical significance as thePDE6Cvariant was detected novel, whereasTULP1,MERTK, andMYO7Avariants were detected rare and first time found segregating with retinal dystrophies in Pakistani consanguineous families.ConclusionsThis study increases knowledge of the genetic basis of retinal dystrophies in families from Pakistan providing information important for genetic testing and diagnostic provision particularly from the Khyber Pakhtunkhwa region.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12886-023-02948-8.