The objective of this study was to investigate the accuracy of imputation from low (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cows with complete pedigree information (n = 1,110) from 129 dairy farms were genotyped with GeneSeek GGP20K (n = 570) and GGP26K (n = 540) BeadChips. After checking for genotypic quality, 16,387 SNP in common between the GGP20K and GGP26K were used to represent MDC in this study. Cows were divided into 2 groups, a reference group (n = 778) and a test group (n = 332). The SNP genotypes chosen for the test group were those SNP located in positions corresponding to GeneSeek GGP9K (n = 7,356). The LDC to MDC genomic imputation was carried out using 3 different methods, namely a population-based algorithm in the Beagle software (PBG), a population-based algorithm in the FImpute software (PFI), and a combined family and population-based algorithm in FImpute (CFI). Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed genotypes to overall imputed genotypes. Imputation accuracy for the 3 methods ranged from 76.31% to 93.91%. The CFI had slightly higher imputation accuracy (93.91%) than PFI (93.56%) and both methods were substantially more accurate than PBG (76.31%). Noticeably most chromosomes that showed either high or low imputation accuracies were the same chromosomes that had high and low average linkage disequilibrium (defined here as the correlation between pairs of adjacent SNP within chromosomes less than 5 MB apart). This suggested that choosing sets of SNP with high levels of average linkage disequilibrium would improve imputation accuracy. Results clearly indicated that FImpute software (population or combined family-population) were more suitable than Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by discarding SNP with low levels of average linkage disequilibrium, and by increasing the completeness of pedigree information.