Swine dysentery (SD) is a disease primarily of grower/finisher pigs typically characterized by colitis and mucohaemorrhagic diarrhoea. The classical aetiological agent is the anaerobic spirochaete Brachyspira hyodysenteriae. In recent year changes to this paradigm have occurred. Firstly, the related species “Brachyspira hampsonii” and Brachyspira suanatina have been identified as causing SD in North America and Europe. Secondly, there have been cases where strains of B. hyodysenteriae have been recovered from pigs in healthy multiplier herds. This study aimed to determine whether cases of SD in Australia might be being caused by the newly described species; to investigate strains of B. hyodysenteriae from healthy herds and compare these with strains from herds with disease; and to compare contemporary isolates with those recovered in previous decades. In total 611 faecal and colonic samples from pigs in 89 herds were collected and tested. Only B. hyodysenteriae was found, and it was present in 27 (30.3%) herds, including 11 (41%) that showed either no signs of disease or mild signs not attributed to SD. Some of these herds previously either had given apparently “false positive” reactions in a serological ELISA for SD, or had epidemiological links to such herds. The other 16 infected herds had a history of having had SD in the recent past or had relevant clinical signs. There was good agreement between a lack of virulence-associated plasmid genes and origin from herds with no or mild disease. Multilocus sequence typing on a subset of isolates revealed that they were diverse and distinct from earlier Australian isolates dating from the 1980s through 2010s, or from those from other countries. Minimum spanning trees suggested there has been a gradual evolution of strains away from those that were recorded in the 1980s. Related isolates were found in some herds with epidemiological links. Resistance to key antimicrobials tiamulin and lincomycin occurred more commonly than in earlier Australian studies, and three multi-drug resistant isolates were identified.