Why do I feel like I'm losing muscle?

1. You muscle losses are minimal, if any.

2. If you want your muscle mass to be "apparent," you should lift weights.

Are you only eating the 1600? you're going to lose a mixture fat, muscle and bone density doing all that cardio unfuelled.

I'd try eating back at least a portion of what you burn.....and add some form of progressive resistance, heck replace a couple of your cardio workouts with it.

Incase you check out my diary and notice I'm only eating 1680 and think I'm being a bit hypocritical - I'm an avid cardio dodger :laugh: - not knocking it, I know I should definitely do some.

I have been loving MFP for the last 100 or so days! Like clockwork, once I saw a nutritionist, I have met my goal of losing 1-1.5 lbs per week and am so far down 20lbs. I have had a very regular 5-day per week workout routine for over a year (5- 30 min cardio on amt elliptical and following 3 of those with 1 hour strength pilates), since long before starting MFP. My nutritionist has me not adding back in my workout calories and I have never not had a deficit during that 100 days. I have always been very strong because of the pilates classes which are gruelling classes with lots of weights and various other torture devices. However, after 100 days of deficit (eating about 1600 calories per day at 5'5") I have noticed my muscles seeming much smaller along with my body weight. Is too little protein the culprit? There is plenty of fat for my body to use without attacking the muscle I have worked so hard to build. Shouldn't my muscle mass be more apparent now rather than the opposite?

Are you seeing a personal trainer as well as a nutritionist? If so, your personal trainer should be telling you that you need rest days in order to build muscle. You need to build a plan that allows you to overload your muscle, then rest it so it can recover and build. If you work your muscles one day after another, they are going to shrink. That's why people who strength train take rest days. Even marathon runners take rest days, and after long marathons have to eat a lot more and rest a lot more to recover. Building up to a place of stamina requires rest too, because the things that help you have stamina are also your muscles.

Another point worth mentioning, you say "there is plenty of fat for my body to use without attacking the muscle I have worked so hard to build." That's actually not always the case. If you are doing aerobic activity that is mild to moderate, the energy system used is the aerobic system and your body will burn fat. However, if you are using an anaerobic energy system you are just going to be burning carbs, and strength training only burns carbs, not fats.
Unfortunately, if you do not eat enough carbs, your body IS going to turn to your protien stores before it turns to fat. That's because your body does not store a lot of carbs, and it burns a lot of carbs very fast. It does however store a lot of fat. That's why carbs are the most important form of fuel for anyone, let alone athletes.

Generally if you are reducing your caloric intake you are going to be weaker. You may not be losing muscle, but you are going to feel weaker. Because it's not healthy. If you want to lose weight, be strong, be fit and be healthy, then do it in a healthy way without dieting and reducing your calories.