Using micro-Raman scattering we have studied atomic distribution and the ordering effects in GaN-rich GaNP layers on (0001) sapphire substrates grown by electron cyclotron resonance molecular beam epitaxy (ECR-MBE). Raman spectrum from layers grown at higher temperatures (≥700°C) shows coexistence of GaP-rich region with cubic symmetry and GaN-rich region with hexagonal symmetry. Sharp TO and LO phonon lines, indicative of {111} ordering in the GaP region are observed. Increasing phosphorous (P >1.5%) in GaNP alloy leads to phase separation that is reflected in the suppression of GaN-like Raman modes. The phase-separated region shows an additional Raman line at 384 cm−1 between the TO and LO phonon of GaP due to strongly confined LO phonon in ordered {111} (GaP)n(GaN)m nanometer size clusters. Decreasing growth temperature increases the phosphorous concentration in the GaNP layer and disorder activated acoustic modes appear in the Raman spectrum as a result of symmetry break down. When phosphorous concentration reaches 8.2 % in the layer grown at 570°C, Raman spectrum shows broad amorphous like bands indicative of short-range ordering