The present invention relates generally to photovoltaic systems. The present invention relates more particularly to photovoltaic roofing systems in which photovoltaic elements are disposed upon roofing elements such as shingles, tiles, shakes or slates. For example, in one embodiment, the present invention provides a photovoltaic roofing system for use on a roof deck, the photovoltaic system including a plurality of horizontally-arranged first photovoltaic roofing elements disposed on the roof deck, each having a top end and a bottom end; one or more first flashing elements disposed on the roof deck upwards from the first photovoltaic roofing elements, the first flashing element having a top end, and a bottom end overlapping the top end of one or more of the first photovoltaic roofing elements; and a plurality of horizontally-arranged second photovoltaic roofing elements disposed on the roof deck upwards from the one or more first flashing elements, each second photovoltaic roofing element having a top end, and a bottom end overlapping the top end of one or more of the first flashing elements, the second photovoltaic roofing elements not overlapping the bottom end of any of the first flashing elements.