Praziquantel (PZQ) is the only drug available to treat schistosomiasis, which is caused by schistosome blood flukes. In Schistosoma mansononi, the transient receptor potential (TRP) channel Sm.TRPMPZQ is strongly suspected to be the target of PZQ. Our genetic analysis of S. mansoni response to PZQ revealed a QTL on its chromosome 3 which contains the Sm.TRPMPZQ gene, strongly suggesting that Sm.TRPMPZQ could be responsible for PZQ resistance. Therefore, understanding the natural variation in this gene and identifying potential resistance alleles will be a valuable tool for monitoring mass treatment programs aimed at schistosomiasis elimination. We investigated our schistosome collection to examine mutations present in Sm.TRPMPZQ in natural schistosome populations. We analyzed exome sequencing data from 259 miracidia, cercariae or adult parasites from 3 African countries (Senegal, Niger, Tanzania), the Middle East (Oman) and South America (Brazil). We were able to sequence 36/41 exons of Sm.TRPMPZQ from 122/259 parasites on average (s.e. = 18.65). We identified several mutations in critical areas of the channel. However, these mutations were supported by a limited number of reads only and required confirmation by Sanger sequencing. The present dataset corresponds to the sequencing effort done on specific exons which carried the mutations to be confirmed. We generated PCR products which were sequenced on on ABI sequencer using Eurofins Genomics services. The SCF files were then analyzed using PolyPhred (see manuscript for details about PCR conditions and data analysis). The trace files are available in the traces folder. Each filename carries a barcode which corresponds to a combination of sample, exon, and primer. All the combinations and corresponding barcodes are listed in the barcode_list.tsv file. Table header details of the barcode list: Sample: the name of sample. The sample coding is as follows: species.country_patientID. BR: Brazil, SN: Senegal, NE: Niger, TZ: Tanzania, OM: Oman. Exon: the exon targeted. The exon number corresponds to the exon number of isoform 5 and not the exon number of the gene. Barcode: the barcode provided by Eurofins Genomics. Primer: the primer used for sequencing. F: forward, R: reverse.