Both have similar functional groups so what causes Nylon 2,6 to be biodegradable while Nylon 6,6 is not?
Biodegradation of polymers generally requires three conditions:
There must be a way to break the high MW polymer molecules down into smaller MW pieces. With condensation polymers like polyesters and polyamides, the logical break points are the ester or amide bonds, which are broken by hydrolysis. Breaking a polyolefin such as polyethylene is much harder and usually is done by oxidation.
The break point must be accessible by an enzyme and any required co-substrate in order for the reaction to happen. In the case of polyamides, this means some sort of amide hydrolase enzyme and water.
The resulting low MW product must be able to be metabolized by microorganisms. With most non-aromatic small organic monomers, this is the easiest step, especially if the monomers are aliphatic acids and amines, as they are for simple polyamides. An example of monomers that cannot be metabolized is halogenated organics such as perfluoroalkanoic acids, where the fluorine atoms interfere with the reactions necessary for breakdown.
For most organic plastics, the first condition is the hardest to satisfy. In particular, polymers with high crystallinity are resistant to degradation because enzymes cannot access the bonds. Similarly, highly hydrophobic polymers are more resistant to hydrolytic degradation because water is excluded from the structure.
As an example, cellulose, which is highly crystalline, is not biodegraded as easily as starch, which is non-crystalline. Among plastics, nylon 6,6 (Tm ~ 250 C, Tg ~ 55 C) is much harder to degrade biologically than poly-$\epsilon$-caprolactone (Tm ~ 60 C, Tg ~ -60 C).
I was unfortunately unable to find a value for the melting temp or glass transition temp of nylon 2,6, but I am confident that those values are much lower than for nylon 6,6, indicating a more amorphous structure which is more amenable to enzymatic hydrolysis to soluble oligomers and monomers.