The transition metal ions responsible for colour in ruby and emerald are, respectively: 

A ruby is a crystal of alumina, aluminum oxide (Al₂O₃) containing a trace of chromium (III) ions replacing some of the aluminum ions. In ruby, each Al³⁺ ion and Cr³⁺ ion is surrounded by six oxide ions in an octahedral arrangement. The origin of the color of emeralds is similar to that of the color of rubies. However, the bulk of an emerald crystal is composed of beryl, beryllium aluminum silicate $\left({\mathrm{Be}}_3{\mathrm{Al}}_2{\left({\mathrm{SiO}}_3\right)}_6\right)$ instead of the alumina which forms rubies. The color is produced by chromium(III) ions, which replace some of the aluminum ions in the crystal. In emeralds, the Cr³⁺ is surrounded by six silicate ions, rather than six oxide ions in ruby. Therefore, the color(green) of emeralds is different from that of ruby.