You can choose to value at market or sale. What this means is that you can either treat your shares as stock - like selling apples - and value them at their value at the end of the financial year - in effect do a stock take.
If you do this you need to keep track of what price you valued them at as a starting point for the next financial year.
Alternatively you can value them at the price you sold them at.
So lets say you have BHP for 10 years. This means you can each year put on your tax returns over those 10 years the gain (or loss)
or you just account for them once at the end when you sell them.
You can mix and match your portfolio - value some one way and some the other.
You can mix and max one share - value them as stock on hand for some years and then elect to value the last few years as a single at sale value.
In the end what the tax department wants is for it all to add up. They don't want to force you to sell all your shares to cover the tax on the capital gain of the shares.
But talk you your accountant - and do a check of the ATO website - I had the reference the other day but cant find it (without a lot of searching) at the moment - I am sure you can use google as well as me. Look for "ATO Share Valuation Market Sale Tax etc etc etc".
