The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or resistance against pathogens, and for performances in production traits. Using dense genomic markers from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5% and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21 and 22. Screening for F_ST outliers in trypanosome positive/ negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative SNPs for routine admixture testing.  Generally, results will serve as basis for further characterization, conservation and improvement strategies for purebred and crossbred populations. Our results are important not only for conserving the genetic integrity in the indigenous Baoulé cattle, but also for improving community-based breeding programs to increase trypanotolerance in crossbred populations.