Aluminium (Al3+) tolerance is second only to drought tolerance for its importance as an agronomic trait in many parts of the world. In wheat (Triticum aestivum L.), Al3+ tolerance is largely conditioned by a single gene, TaALMT1, but given the diverse origins of tolerant genotypes, it is possible that other chromosomes may harbour genes that confer Al3+ tolerance. The large genetic diversity present in synthetic hexaploid wheat (SHW) prompted the objective in this study, which was to evaluate SHW as a source of novel genetic loci linked to Al3+ tolerance. We evaluated 300 SHW accessions using the haematoxylin staining method, and a genome-wide association analysis (GWAS) using 6575 markers generated from traditional diversity-arrays and genotyping-by-sequencing genotyping platforms and from TaALMT1 gene specific simple sequence repeat polymorphisms. The GWAS detected a set of 24 loci located to chromosomes 1B, 1D, 2A, 2B, 4A, 4D, 5A, 5B, 6A, 6D and 7A that showed statistically significant association with Al3+ tolerance. We leveraged the available high-quality annotation data of the wheat genome to identify candidate genes localised to within 1.6 Kb of the identified markers. Besides markers for TaALMT1, MATE and NRAMP, identified markers were located close to known transcription factors (C2H2 zinc finger protein) and novel candidate genes that encode ABC transporter-like protein, glutathione synthetase, Blue copper protein and expansin proteins. In summary, our results showed that Al3+ tolerance is present in SHW but is genetically complex and appeared to involve interactions between the major TaALMT1 gene and other gene loci.