Squash (Cucurbita pepo L.) is one of the most commonly cultivated crops in Turkey. In recent years, with the decrease in rainfall and the increase in irrigation costs, there has been an increased interest in edible seed squash cultivation in Turkey, since it can be grown well in arid environments. Virus diseases are the most common problem limiting edible seed squash cultivation in Turkey. During 2017–2019, 625 symptomatic edible seed squash leaves were collected from the fields for detection of pathogenic viruses, including watermelon mosaic potyvirus (WMV), Zucchini yellow mosaic potyvirus (ZYMV), cucurbit aphid-borne yellows polerovirus (CABYV), squash mosaic comovirus (SqMV), cucumber mosaic cucumovirus (CMV), and papaya ringspot potyvirus watermelon strain (PRSV-W) using DAS-ELISA and RT-PCR methods. The calculated relative incidence of viruses infecting plant samples was found to be 88.32%. WMV, ZYMV, and CABYV were identified as the most prevalent viruses with the relative incidences of 56.96, 56, and 20.16%, respectively. CMV (1.12%), PRSV-W (0.48%), and SqMV (0.32%) were the least commonly detected viruses in samples. The 24 selected isolates of CMV (2), WMV (12), ZYMV (6), and CABYV (4) were sequenced and deposited in the GenBank database. The phylogenetic analysis revealed that Turkish isolates of these viruses belong to the same clusters in phylogenetic trees and generally showed high similarities to the isolates of neighboring countries. Moreover, except for the CABYV isolates, the sequence diversity among the isolates was generally very low. It is thought that the knowledge gained from observations of this study will be useful to beneficiaries as it provides a basis for further research into the breeding programs of squash varieties resistant to virus diseases.