For the first time, the co-templating ionothermal methodology was used in the preparation of layered aluminophosphate materials. With the addition of either 1,2-ethylenediamine or 1,6-hexanediamine to the ionic liquid 1-ethyl-3-methyl imidazolium chloride, two new 2D layered aluminophosphates RUB-A1 [Al3P4O16][NH3CH2CH2NH3]0.5[C6N2H11]2 and RUB-A2 [Al3P4O16][NH3(CH2)6NH3][NH3(CH2)6NH2]0.5[C6N2H11]0.5[H2O] have been synthesized ionothermally by co-templating. The structure of RUB-A1 has been determined from single-crystal X-ray diffraction data using direct methods, while the structure of RUB-A2 has been solved ab initio from powder X-ray diffraction data with limited resolution using direct-space methods. Both of these two compounds have a 2D layered structure consisting of macroanionic sheets of composition [Al3P4O16]3− stacked in an AAAA sequence. The inorganic layers are built up from alternatively vertex-sharing [AlO4]- and [PO3(O)]-tetrahedral units forming a 4.6.8 and a 4.6.12 network for RUB-A1 and RUB-A2, respectively. The layer topology of RUB-A1 is closely related to the previously known 4.6.8-layer topology but with a different sequence of phosphoryl group orientation. Combining the results of structure analysis with the NMR, chemical analysis and TG-DTA experiments, we show that both the ionic liquid cation and the protonated diamines are located in the interlayer space and together direct the formation of these two structures.