Fodd bynnag, mae'r dystiolaeth yn dangos bod nifer fach o ddiffygion o ran cynefinoedd yn ein rhwydwaith, yn bennaf yn ardaloedd dwfn y môr mawr, y mae angen eu hystyried i gwblhau ein rhwydwaith o MPAau. Ar hyn o bryd dim ond un Parth Cadwraeth Morol (MCZ) sydd wedi cael ei ddynodi yng Nghymru, sef Sgomer.  Mae dynodi Sgomer yn MCZ wedi ei galluogi i elwa ar fesurau o dan ddeddfwriaeth cadwraeth natur i gyfyngu ar weithgareddau, er enghraifft defnyddio offer pysgota symudol a chymryd, lladd neu darfu ar fywyd gwyllt. Mae hefyd terfyn cyflymder o 5 not o fewn 100 metr o'r traeth i leihau tarfu ar fywyd gwyllt.
Evidence does, however, demonstrate there remain a small number of habitat shortfalls in our network, predominantly in the deeper offshore, requiring consideration to complete our MPA network. Currently, we have only one Marine Conservation Zone (MCZ) designated in Wales, Skomer.  Designating Skomer as an MCZ has enabled it to benefit from measures under nature conservation legislation to restrict activities Designating Skomer as an MCZ has enabled it to benefit from measures under nature conservation legislation to restrict activities such as the use of mobile fishing gear and the taking, killing or disturbing of wildlife. There is also a 5-knot speed limit within 100m of the shore to reduce disturbance to wildlife.