Quantitative trait locus (QTL) mapping studies have been integral in identifying and understanding virulence mechanisms in the parasite Toxoplasma gondii. Here, we interrogate a different phenotype by mapping sinefungin (SNF) drug resistance in the genetic cross between type 2 ME49-FUDRR and type 10 VAND-SNFR. The genetic map of this cross was generated by whole-genome sequencing of the progeny and subsequent identification of SNPs inherited from the parents. Based on this high density genetic map, we were able to pin point the sinefungin resistance phenotype to one significant locus on chromosome IX. Within this locus, a single non-synonymous SNP (nsSNP) resulting in an early stop codon in the TGVAND_290860 gene was identified occurring only in the sinefungin resistant progeny. Using CRISPR/CAS9 we were able to confirm that targeted disruption of TGVAND_290860 renders parasites sinefungin resistant. Because disruption of the SNR1 gene confers resistance, we also show that it can be used as a negative selectable marker to insert either a positive drug selection cassette or a heterologous reporter. These data demonstrate the power of combining classical genetic mapping, whole genome sequencing, and CRISPR mediated gene disruption for combined forward and reverse genetic strategies in T. gondii.