Linkage disequilibrium (LD) is important for gene mapping, accuracy of genomic prediction, and understanding of recombination biology in dairy cattle populations. The level of LD can vary among populations depending on their genetic structure, selection and recombination rates. The objective of this study was to estimate and compare levels of LD in dairy cattle with different Holstein fractions under tropical conditions. Blood samples of 2,643 dairy cattle (89 bulls and 2,554 cows) from 304 farms located in Central, Northern, Western and Southern Thailand were extracted for DNA. The DNA samples were genotyped with one of 4 GeneSeek Genomic Profiler BeadChips (9K, 20K, 26K, or 80K). Only SNPs from autosomes in common among the 4 chips were considered. In addition, SNPs with a minor allele frequency (MAF) lower than 0.01 and a call rate lower than 90% were excluded. This resulted in a set of 7,123 SNPs used in this study. Animals were classified into 7 groups based on their Holstein fraction (HF): HF <75%, 75% ≤ HF <80%, 80% ≤ HF <85%, 85% ≤ HF <90%, 90% ≤ HF <95%, 95% ≤ HF <100%, and purebred HF. Distribution of MAF and estimation of LD were done using Haploview. All HF groups had similar patterns of MAF across autosomes (fraction of SNPs increased with an increase in MAF). However, means of MAF across autosomes differed among HF groups and it tended to decrease with an increase in H fraction (from 0.376 for HF <75% to 0.362 for purebred HF). Conversely, the mean r² across autosomes tended to increase as HF increased from 0.081 for HF <75% to 0.109 for purebred HF. Results from this study will be useful for genome wide association studies and for genomic prediction and selection of crossbred Holstein cattle in tropical regions.