They can be near impossible to tell the difference when frags, but I find when they grow out Millis tend to table and Prostratas will branch out more. More details in these two links.
There are a few key differences that I am aware of.
1. branch thickness and length; A. millepora have "short uniform branches", A. prostrata have "thin elongate branches" (Veron)
2. colony structure: A. millepora: form corymbose cushions, A. prostrata: form both corymbose and irregular cushions. Veron also uses the word "clump" to describe A. prostrata. I believe this may be referring to the open structure that the species exhibits. For me, this is one of the better traits to use to distinguish the species.
3. corallite spacing: both species are described as having a "scale-like appearance" which causes all sorts of identification issues, but only A. millepora have closely compacted radial corallites.
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