We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony to impute data marked as missing due to low coverage. Along with efficiently imputing missing variant genotypes, IMPUTOR is capable of reliably and accurately correcting many nonmissing sites that represent spurious sequencing errors. Tests on simulated data show that IMPUTOR is capable of detecting many induced mutations without making erroneous imputations/corrections, with as many as 95% of missing sites imputed and 81% of errors corrected under optimal conditions. We tested IMPUTOR with human Y-chromosomes from pairs of close relatives and demonstrate IMPUTOR's efficacy in imputing missing and correcting erroneous calls.