Several distinct, naturally occurring colour varieties are recognised as haplotypes, each found in a specific geographic region. They include:
- The green is the most common variety, found in Indonesia (Kalimantan and Sumatra), Vietnam, Myanmar, Thailand,Cambodia, and Malaysia.
- The silver Asian (not to be confused with the silver arowana, Osteoglossum bicirrhosum) is considered part of the green variety by some. It has two subvarieties, the "grey tail silver" or "Pinoh arowana," and the "yellow tail silver," each found in a different part of the island of Borneo in Indonesia.
- The red-tailed golden is found in northern Sumatra, Indonesia.
- The gold crossback, blue Malayan, or Bukit Merah blue is native to the state of Pahang and the Bukit Merah area in Perak,Peninsular Malaysia.
- The red, super red, blood red, or chili red is known only from the upper part of the Kapuas River and nearby lakes in western Borneo, Indonesia.
- Scleropages formosus was redescribed to include the strain known as the green arowana. The gold crossback, which was not part of the study, was included in this species by default, though it was suspected to be closely related to S. aureus.
- Scleropages macrocephalus described the silver Asian arowana.
- Scleropages aureus described the red-tailed golden arowana.
- Scleropages legendrei described the super red arowana.