The larger sarsens come from nearby Marlborough Downs and the smaller bluestones from the Preseli mountains in Pembrokeshire, but the sandstone of the main Altar Stone is foreign to both areas.
Richard Bevins of the Museum of Wales and Rob Ixer of the University of Leicester say the main Altar Stone 'very probably' came from the Senni Beds, which stretch from Llanelli to Herefordshire, according to The Times.
Researchers first thought it was transported by boat, but now believe roads and rivers may have been used.
Their new theory is that it was first hauled to Monmouth and the lower parts of the River Monmouth with animals and rollers, then somehow crossed the River Severn, or was rafted down to Avon.
Writing in the journal Antiquity, Richard Bevins of the Museum of Wales and Rob Ixer of the University of Leicester claim a route first proposed by geologist H.H. Thomas in 192, that saw the transport of the Stonehenge bluestones from the Mynydd Preseli area of north Pembrokeshire is wrong.
"New analytical techniques, alongside transmitted and reflected light microscopy, have recently prompted renewed scrutiny of Thomas' work," they wrote.
They also say his sourcing of the bluestones was wrong.
"While respectable for its time, the results of these new analyses, combined with a thorough checking of the archived samples consulted by Thomas, reveal that key locations long believed to be sources for the Stonehenge bluestones can be discounted in favour of newly identified locations at Craig-Rhos-y-felin and Carn Goedog," they say.
HOW WAS STONEHENGE BUILT?
Stonehenge is one of the most prominent prehistoric monuments in Britain. The Stonehenge that can be seen today is the final stage that was completed about 3,500 years ago.
According to the monument's website, Stonehenge was built in four stages:
First stage: The first version of Stonehenge was a large earthwork or Henge, comprising a ditch, bank and the Aubrey holes, all probably built around 3100 BC.
The Aubrey holes are round pits in the chalk, about one metre (3.3 feet) wide and deep, with steep sides and flat bottoms.
They form a circle about 86.6 metres (284 feet) in diameter.
Excavations revealed cremated human bones in some of the chalk filling, but the holes themselves were likely not made to be used as graves, but as part of a religious ceremony.
After this first stage, Stonehenge was abandoned and left untouched for more than 1,000 years.
Second stage: The second and most dramatic stage of Stonehenge started around 2150 years BC, when about 82 bluestones from the Preseli mountains in south-west Wales were transported to the site. It's thought that the stones, some of which weigh four tonnes each, were dragged on rollers and sledges to the waters at Milford Haven, where they were loaded onto rafts.
They were carried on water along the south coast of Wales and up the rivers Avon and Frome, before being dragged overland again near Warminster and Wiltshire.
The final stage of the journey was mainly by water, down the river Wylye to Salisbury, then the Salisbury Avon to west Amesbury.
The journey spanned nearly 240 miles, and once at the site, the stones were set up in the centre to form an incomplete double circle.
During the same period, the original entrance was widened and a pair of Heel Stones were erected. The nearer part of the Avenue, connecting Stonehenge with the River Avon, was built aligned with the midsummer sunrise.
Third stage: The third stage of Stonehenge, which took place about 2000 years BC, saw the arrival of the sarsen stones (a type of sandstone), which were larger than the bluestones.
They were likely brought from the Marlborough Downs (40 kilometres, or 25 miles, north of Stonehenge).
The largest of the sarsen stones transported to Stonehenge weighs 50 tonnes, and transportation by water would not have been possible, so it's suspected that they were transported using sledges and ropes.
Calculations have shown that it would have taken 500 men using leather ropes to pull one stone, with an extra 100 men needed to lay the rollers in front of the sledge.
These stones were arranged in an outer circle with a continuous run of lintels - horizontal supports.
Inside the circle, five trilithons - structures consisting of two upright stones and a third across the top as a lintel - were placed in a horseshoe arrangement, which can still be seen today.
Final stage: The fourth and final stage took place just after 1500 years BC, when the smaller bluestones were rearranged in the horseshoe and circle that can be seen today.
The original number of stones in the bluestone circle was probably around 60, but these have since been removed or broken up. Some remain as stumps below ground level.