Each and every Pilates instructor will have been asked this countless times and there are all manner of things written on the Internet trying to answer it. Let’s have a look at some of the common thoughts on what the difference between Pilates and Yoga is. For clarity I am focusing on Yoga as an ‘exercise system’ and not the ‘belief system’ it actually is.
Pilates focuses on strength whereas Yoga focuses on flexibility
Both of these exercise systems focus on both of these areas. Pilates has a strong focus on flexibility using movement, as well as static poses which are often taken from Yoga. Yoga most definitely also focuses on strength in nearly all of it’s disciplines, but heavily in Ashtanga.
Yoga is spiritual, whereas Pilates isn’t
Yes, yoga is heavily grounded in spirituality. It is to be used as part of a whole spiritual practice, but probably the majority of Western practitioners do not partake in all the other Vedic practises. Pilates is not often seen as spiritual, but if you read Joseph Pilates’ original text he states ‘Contrology [Pilates] is complete coordination of mind, body and spirit.’  I had a Yoga teacher say to me the other day that they ‘didn’t realise that Pilates was spiritual’. My response was that anything is spiritual…if you are spiritual. Therefore if you aren’t a spiritual person, Yoga will not be spiritual to you. If you are a spiritual person, Pilates can be spiritual to you.
Pilates classes are more structured, whereas Yoga is more flexible and varied
Pilates stems from 34 original exercises , but today has a far wider variety. Depending on your Pilates teachings, you can apply any number of different exercises, stretches, poses etc. as long as you apply the principles of Pilates (read here for the principles of Pilates). The original Yoga Sutra only mentions asanas (poses) twice, and the oldest documentation of Hatha Yoga states only 15 asanas . Both Pilates and Yoga stem from quite strict backgrounds and have massively changed today.
Yoga focuses on global muscles, whereas Pilates focuses on the smaller, stabilising muscles
In order to get into asanas in Yoga correctly you are required to use stabilising muscles. It is what makes them challenging for many. Pilates does focus on these muscles, but it will also use global muscles. The level of which they are used depends on the class you attend, which equally applies to Yoga. Go to a Yin Yoga class and you are actually trying to minimise muscle involvement.
I do both Pilates and Yoga, and know they are different practises but to put precisely the difference is very difficult. The differences that most people seem to state are generalise the two practices in order to compare, which I don’t think do them justice. As a Pilates instructor I will try to be impartial, but for me the actual differences are these:
Pilates is often marketed as either for rehabilitation or for helping back pain, Yoga marketed for spiritual gain. This to me is solely marketing. Yoga can relieve back pain and rehabilitate, Pilates can give spiritual benefits. I do not want to offend any true Yogis/Yoginis, but Yoga in the West is very different to the practise in the East; we now see Yoga with dogs, drinking Yoga and all sorts! Whilst classes may still help give a spiritual perspective, they alone will not change your mindset. The same applies to Pilates and rehabilitation; you also need to apply the principals to your everyday life to reap rewards.
Yoga can be said to originate from as early as 300 c.e.  and Pilates from 1926. It was coincidentally around the same time, 1920, that Yoga was introduced to the West . This explains why Joseph Pilates actually used Yoga asanas, but applied his Contrology (Pilates) methodology to them.
Who teaches you
This for me is what will make the biggest difference in the experience you have with either of these. Every teacher has their own ways and focuses. Some Pilates instructors focus more on the breath than the precision, some Yoga instructors focus more on the spirituality than the alignment and so on. I’ve had some wonderful Pilates instructors who have ended classes with ‘hands on heart centre’ and a namaste, and I’ve had Yoga instructors come and correct positioning with precision. Who teaches you will effect your experience of each ‘system’, so find instructors who suit you.
None of this probably helps you decide between the two, but that is my point. You don’t need to pick sides, you can use both for different or the same reasons. I believe in a lot of ‘Eastern’ practices including the importance of a balance of Yin and Yang in our lives. Pilates became my Yang practise, and Yin Yoga my…Yin!