There is no reason why such a species could not evolve. The main reason for anisogamy is that it provides the less-common gamete with the resources that the progeny will require for growth after fusion with a more-common gamete, minimising wastage of the parental investment.
Organ differentiation occurs in order to increase the efficiency of the various metabolic tasks the organism must undertake. The two criteria are not mutually exclusive.
In order to retain isogamy, the environment must support it. This means that internal fertilisation is probably out of the question, since that favours an anisogamous sessile egg/motile sperm arrangement. External fertilisation in water (like river or sea water) is also probably out of the question, as anisogamy has its advantages there too, in that the egg can carry resources for the developing organism while the sperm can be plentiful.
The most likely environment is one where there is an abundance of all the nutrients that the developing organism will need. In such an environment, the gametes may remain small and motile so that they can move around in an attempt to find an opposite gamete.
Of course, unless you want a system that strongly favours autogamy, there will have to be a small degree of anisogamy, but only to the degree that gametes are only attracted to other gametes if they are of the opposite type (i.e. + vs -, to eliminate gender-biased labels), or able to distinguish between sibling and non-sibling gametes, though that would be much more complicated. However apart from that the gametes would be functionally identical.
Reproduction would most likely involve the parents each contributing to a pool of liquid nutrients in which a number of offspring could develop, before each inserting a similar number of gametes.
This does not preclude being functional in a liquid environment as opposed to a terrestrial environment. In any environment, this method of reproduction would require that the nutrients be isolated from the surrounding environment in order to prevent infection by foreign microorganisms and from being eaten by larger organisms - it is a packet of nutrients, after all.
The parents would most likely each contribute equally to building - or being the container for the nutrient soup, though the possibility exists that one parent would end up responsible for caring for the whole thing, or more likely that each parent would form their own nutrient pool and add their gametes to both their own and their partner's. Alternatively, both parents contribute to building a container, and finally add their gametes and then abandon it in as safe a place as they can find.